fhR-4.4.2-foss-2024a-R-4.4.2.eb

Known Issues

• None

Package List

• ALDEx2-1.38.0 Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
• ALL 1.46.0 Package Not Found
• AgiMicroRna-2.56.0 Processing and Differential Expression Analysis of Agilent microRNA chips
• AnnotationDbi-1.68.0 Manipulation of SQLite-based annotations in Bioconductor
• AnnotationFilter-1.30.0 Facilities for Filtering Bioconductor Annotation Resources
• AnnotationForge-1.48.0 Tools for building SQLite-based annotation data packages
• AnnotationHub-3.14.0 Client to access AnnotationHub resources
• ArchR 1.0.2 Package Not Found
• BSgenome-1.74.0 Software infrastructure for efficient representation of full genomes and their SNPs
• BSgenome.Hsapiens.UCSC.hg19 1.4.3 Package Not Found
• Bhat-0.9-12 General Likelihood Exploration
• Biobase-2.66.0 Biobase: Base functions for Bioconductor
• BiocBaseUtils-1.8.0 General utility functions for developing Bioconductor packages
• BiocFileCache-2.14.0 Manage Files Across Sessions
• BiocGenerics-0.52.0 S4 generic functions used in Bioconductor
• BiocIO-1.16.0 Standard Input and Output for Bioconductor Packages
• BiocManager-1.30.25 Access the Bioconductor Project Package Repository
• BiocNeighbors-2.0.1 Nearest Neighbor Detection for Bioconductor Packages
• BiocParallel-1.40.0 Bioconductor facilities for parallel evaluation
• BiocSingular-1.22.0 Singular Value Decomposition for Bioconductor Packages
• BiocStyle-2.34.0 Standard styles for vignettes and other Bioconductor documents
• BiocVersion-3.20.0 Set the appropriate version of Bioconductor packages
• Biostrings-2.74.1 Efficient manipulation of biological strings
• BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
• Bolstad-0.2.42 Functions for Elementary Bayesian Inference
• Bolstad2-1.0-29 Bolstad Functions
• BradleyTerry2-1.1-2 Bradley-Terry Models
• CATALYST-1.30.2 Cytometry dATa anALYSis Tools
• CGHbase-1.66.0 CGHbase: Base functions and classes for arrayCGH data analysis.
• CLONETv2-2.2.1 Clonality Estimates in Tumor
• CMA-1.64.0 Synthesis of microarray-based classification
• CNEr-1.42.0 CNE Detection and Visualization
• COMPASS-1.44.0 Combinatorial Polyfunctionality Analysis of Single Cells
• CaSpER v2.0 Package Not Found
• Category-2.72.0 Category Analysis
• ChIPQC-1.42.0 Quality metrics for ChIPseq data
• ChIPpeakAnno-3.40.0 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
• ChIPseeker-1.42.1 ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
• ComplexHeatmap-2.22.0 Make Complex Heatmaps
• ConsensusClusterPlus-1.70.0 ConsensusClusterPlus
• CytoML-2.18.2 A GatingML Interface for Cross Platform Cytometry Data Sharing
• DAAG-1.25.6 Data Analysis and Graphics Data and Functions
• DECIPHER-3.2.0 Tools for curating, analyzing, and manipulating biological sequences
• DEGseq-1.60.0 Identify Differentially Expressed Genes from RNA-seq data
• DESeq2-1.46.0 Differential gene expression analysis based on the negative binomial distribution
• DNAcopy-1.80.0 DNA Copy Number Data Analysis
• DO.db 2.9 Package Not Found
• DOSE-4.0.0 Disease Ontology Semantic and Enrichment analysis
• DOT-0.1 Render and Export DOT Graphs in R
• DelayedArray-0.32.0 A unified framework for working transparently with on-disk and in-memory array-like datasets
• DelayedMatrixStats-1.28.1 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
• DiceDesign-1.10 Designs of Computer Experiments
• DiffBind-3.16.0 Differential Binding Analysis of ChIP-Seq Peak Data
• DirichletMultinomial-1.48.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
• DynDoc-1.84.0 Dynamic document tools
• EBImage-4.48.0 Image processing and analysis toolbox for R
• EpiModel-2.5.0 Mathematical Modeling of Infectious Disease Dynamics
• ExperimentHub-2.14.0 Client to access ExperimentHub resources
• FDb.InfiniumMethylation.hg19 2.2.0 Package Not Found
• FlowSOM-2.14.0 Using self-organizing maps for visualization and interpretation of cytometry data
• GEOquery-2.74.0 Get data from NCBI Gene Expression Omnibus (GEO)
• GO.db 3.19.1 Package Not Found
• GOSemSim-2.32.0 GO-terms Semantic Similarity Measures
• GOstats-2.72.0 Tools for manipulating GO and microarrays
• GPfit-1.0-8 Gaussian Processes Modeling
• GSEABase-1.68.0 Gene set enrichment data structures and methods
• GSVA-2.0.5 Gene Set Variation Analysis for Microarray and RNA-Seq Data
• GWASExactHW-1.2 Exact Hardy-Weinburg Testing for Genome Wide Association Studies
• GWASTools-1.52.0 Tools for Genome Wide Association Studies
• GenomeInfoDb-1.42.3 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
• GenomeInfoDbData 1.2.12 Package Not Found
• GenomicAlignments-1.42.0 Representation and manipulation of short genomic alignments
• GenomicFeatures-1.58.0 Query the gene models of a given organism/assembly
• GenomicFiles-1.42.0 Distributed computing by file or by range
• GenomicRanges-1.58.0 Representation and manipulation of genomic intervals
• Glimma-2.16.0 Interactive visualizations for gene expression analysis
• Gmisc-3.0.3 Descriptive Statistics, Transition Plots, and More
• GreyListChIP-1.38.0 Grey Lists – Mask Artefact Regions Based on ChIP Inputs
• Gviz-1.50.0 Plotting data and annotation information along genomic coordinates
• HDF5Array-1.34.0 HDF5 datasets as array-like objects in R
• HDO.db 0.99.1 Package Not Found
• HMMcopy-1.48.0 Copy number prediction with correction for GC and mappability bias for HTS data
• HSMMSingleCell 1.24.0 Package Not Found
• HaploSim-1.8.4.2 Functions to Simulate Haplotypes
• Homo.sapiens 1.3.1 Package Not Found
• IHW-1.34.0 Independent Hypothesis Weighting
• IRanges-2.40.1 Foundation of integer range manipulation in Bioconductor
• IRdisplay-1.1 ‘Jupyter’ Display Machinery
• IlluminaHumanMethylation450kmanifest 0.4.0 Package Not Found
• InteractionSet-1.34.0 Base Classes for Storing Genomic Interaction Data
• KEGGREST-1.46.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
• KEGGgraph-1.66.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
• LogicReg-1.6.6 Logic Regression
• LymphoSeq-1.34.0 Analyze high-throughput sequencing of T and B cell receptors
• LymphoSeqDB 0.99.2 Package Not Found
• MAGeCKFlute-2.9.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
• MAST-1.32.0 Model-based Analysis of Single Cell Transcriptomics
• MCMCglmm-2.36 MCMC Generalised Linear Mixed Models
• MPV-1.64 Data Sets from Montgomery, Peck and Vining
• MatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations
• MatrixExtra-0.1.15 Extra Methods for Sparse Matrices
• MatrixGenerics-1.18.1 S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
• Mfuzz-2.66.0 Soft clustering of omics time series data
• NADA-1.6-1.1 Nondetects and Data Analysis for Environmental Data
• NOISeq-2.50.0 Exploratory analysis and differential expression for RNA-seq data
• Nozzle.R1-1.1-1.1 Nozzle Reports
• OrganismDbi-1.48.0 Software to enable the smooth interfacing of different database packages
• PBSddesolve-1.13.4 Solver for Delay Differential Equations
• PFAM.db 3.19.1 Package Not Found
• PICS-2.50.0 Probabilistic inference of ChIP-seq
• PolynomF-2.0-8 Polynomials in R
• ProtGenerics-1.38.0 Generic infrastructure for Bioconductor mass spectrometry packages
• QUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix Estimation
• R2jags-0.8-9 Using R to Run ‘JAGS’
• RBGL-1.82.0 An interface to the BOOST graph library
• REDCapR-1.4.0 Interaction Between R and REDCap
• RLRsim-3.1-8 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive Models
• RNASeqPower-1.46.0 Sample size for RNAseq studies
• RPostgres-1.4.8 C++ Interface to PostgreSQL
• RPresto-1.4.7 DBI Connector to Presto
• RProtoBuf-0.4.23 R Interface to the ‘Protocol Buffers’ ‘API’ (Version 2 or 3)
• RProtoBufLib-2.18.0 C++ headers and static libraries of Protocol buffers
• RSclient-0.7-10 Client for Rserve
• RVenn-1.1.0 Set Operations for Many Sets
• RaggedExperiment-1.30.0 Representation of Sparse Experiments and Assays Across Samples
• RcppAnnoy-0.0.22 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest Neighbors
• RcppCCTZ-0.2.13 ‘Rcpp’ Bindings for the ‘CCTZ’ Library
• RcppDate-0.0.5 ‘date’ C++ Header Library for Date and Time Functionality
• RcppHNSW-0.6.0 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest Neighbors
• RcppML-0.3.7 Rcpp Machine Learning Library
• RcppNumerical-0.6-0 ‘Rcpp’ Integration for Numerical Computing Libraries
• RcppPlanc 1.0.0 Package Not Found
• RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG Implementations
• Rdsdp-1.0.5.2.1 R Interface to DSDP Semidefinite Programming Library
• ReportingTools-2.46.0 Tools for making reports in various formats
• Rfast-2.1.5 A Collection of Efficient and Extremely Fast R Functions
• Rgraphviz-2.50.0 Provides plotting capabilities for R graph objects
• Rhdf5lib-1.28.0 hdf5 library as an R package
• Rhpc-0.21-247 Permits *apply() Style Dispatch for ‘HPC’
• Rhtslib-3.2.0 HTSlib high-throughput sequencing library as an R package
• Rlabkey-3.4.1 Data Exchange Between R and ‘LabKey’ Server
• Rmpi-0.7-3.3 Interface (Wrapper) to MPI (Message-Passing Interface)
• Rsamtools-2.22.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
• Rsubread-2.20.0 Mapping, quantification and variant analysis of sequencing data
• S4Arrays-1.6.0 Foundation of array-like containers in Bioconductor
• S4Vectors-0.44.0 Foundation of vector-like and list-like containers in Bioconductor
• SNPRelate-1.40.0 Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
• SNPassoc-2.1-2 SNPs-Based Whole Genome Association Studies
• SPIA-2.58.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
• ScaledMatrix-1.14.0 Creating a DelayedMatrix of Scaled and Centered Values
• SemiPar-1.0-4.2 Semiparametic Regression
• ShortRead-1.64.0 FASTQ input and manipulation
• SingleCellExperiment-1.28.1 S4 Classes for Single Cell Data
• SparseArray-1.6.2 High-performance sparse data representation and manipulation in R
• SpatialExperiment-1.16.0 S4 Class for Spatially Resolved -omics Data
• SummarizedExperiment-1.36.0 A container (S4 class) for matrix-like assays
• TFBSTools-1.44.0 Software Package for Transcription Factor Binding Site (TFBS) Analysis
• TFMPvalue-0.0.9 Efficient and Accurate P-Value Computation for Position Weight Matrices
• TitanCNA-1.44.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
• TxDb.Celegans.UCSC.ce6.ensGene 3.2.2 Package Not Found
• TxDb.Dmelanogaster.UCSC.dm3.ensGene 3.2.2 Package Not Found
• TxDb.Hsapiens.UCSC.hg18.knownGene 3.2.2 Package Not Found
• TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2 Package Not Found
• TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0 Package Not Found
• TxDb.Mmusculus.UCSC.mm9.knownGene 3.2.2 Package Not Found
• TxDb.Rnorvegicus.UCSC.rn4.ensGene 3.2.2 Package Not Found
• UCSC.utils-1.2.0 Low-level utilities to retrieve data from the UCSC Genome Browser
• VariantAnnotation-1.52.0 Annotation of Genetic Variants
• Wrench-1.24.0 Wrench normalization for sparse count data
• XVector-0.46.0 Foundation of external vector representation and manipulation in Bioconductor
• affxparser-1.78.0 Affymetrix File Parsing SDK
• affy-1.84.0 Methods for Affymetrix Oligonucleotide Arrays
• affycoretools-1.78.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
• affyio-1.76.0 Tools for parsing Affymetrix data files
• alr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Edition
• amap-0.8-20 Another Multidimensional Analysis Package
• annaffy-1.78.0 Annotation tools for Affymetrix biological metadata
• annotate-1.84.0 Annotation for microarrays
• apeglm-1.28.0 Approximate posterior estimation for GLM coefficients
• argparser-0.7.2 Command-Line Argument Parser
• arsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical Summaries
• arules-1.7-9 Mining Association Rules and Frequent Itemsets
• ash-1.0-15 David Scott’s ASH Routines
• ashr-2.2-63 Methods for Adaptive Shrinkage, using Empirical Bayes
• assorthead-1.0.1 Assorted Header-Only C++ Libraries
• aws.ec2metadata-0.2.0 Get EC2 Instance Metadata
• aws.s3-0.3.21 ‘AWS S3’ Client Package
• aws.signature-0.6.0 Amazon Web Services Request Signatures
• babelgene-22.9 Gene Orthologs for Model Organisms in a Tidy Data Format
• bamsignals-1.38.0 Extract read count signals from bam files
• base64url-1.4 Fast and URL-Safe Base64 Encoder and Decoder
• basilisk-1.18.0 Freezing Python Dependencies Inside Bioconductor Packages
• basilisk.utils-1.18.0 Basilisk Installation Utilities
• batchtools-0.9.17 Tools for Computation on Batch Systems
• beachmat-2.22.0 Compiling Bioconductor to Handle Each Matrix Type
• benchmark-0.3-6 Benchmark Experiments Toolbox
• bezier-1.1.2 Toolkit for Bezier Curves and Splines
• biglm-0.9-3 Bounded Memory Linear and Generalized Linear Models
• biomaRt-2.62.1 Interface to BioMart databases (i.e. Ensembl)
• biomformat-1.34.0 An interface package for the BIOM file format
• biovizBase-1.54.0 Basic graphic utilities for visualization of genomic data.
• bookdown-0.42 Authoring Books and Technical Documents with R Markdown
• breakaway-4.8.4 Species Richness Estimation and Modeling
• bumphunter-1.48.0 Bump Hunter
• catdata-1.2.4 Categorical Data
• chipseq-1.56.0 chipseq: A package for analyzing chipseq data
• chromVAR-1.28.0 Chromatin Variation Across Regions
• clusterProfiler-4.14.6 A universal enrichment tool for interpreting omics data
• collections-0.3.7 High Performance Container Data Types
• colorRamps-2.3.4 Builds Color Tables
• compare-0.2-6 Comparing Objects for Differences
• config-0.3.2 Manage Environment Specific Configuration Values
• cummeRbund-2.48.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
• curry-0.1.1 Partial Function Application with %<%, %-<%, and %><%
• cyclocomp-1.1.1 Cyclomatic Complexity of R Code
• cytolib-2.16.0 C++ infrastructure for representing and interacting with the gated cytometry data
• dada2-1.34.0 Accurate, high-resolution sample inference from amplicon sequencing data
• degreenet-1.3-6 Models for Skewed Count Distributions Relevant to Networks
• densvis-1.16.0 Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction
• depmap 1.18.0 Package Not Found
• derfinder-1.40.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
• derfinderHelper-1.40.0 derfinder helper package
• descr-1.1.8 Descriptive Statistics
• dfoptim-2023.1.0 Derivative-Free Optimization
• dials-1.4.0 Tools for Creating Tuning Parameter Values
• diamonds-1.0-5 Analysis and sampling grids from diamond partitions
• diffusionMap-1.2.0 Diffusion Map
• dir.expiry-1.14.0 Managing Expiration for Cache Directories
• directlabels-2024.1.21 Direct Labels for Multicolor Plots
• doFuture-1.0.1 Use Foreach to Parallelize via the Future Framework
• doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
• dqrng-0.4.1 Fast Pseudo Random Number Generators
• drc-3.0-1 Analysis of Dose-Response Curves
• edgeR-4.4.2 Empirical Analysis of Digital Gene Expression Data in R
• egor-1.24.2 Import and Analyse Ego-Centered Network Data
• elasticnet-1.3 Elastic-Net for Sparse Estimation and Sparse PCA
• enrichplot-1.26.6 Visualization of Functional Enrichment Result
• ensembldb-2.30.0 Utilities to create and use Ensembl-based annotation databases
• ergm.ego-1.1.0 Fit, Simulate and Diagnose Exponential-Family Random Graph Models to Egocentrically Sampled Network Data
• etrunct-0.1 Computes Moments of Univariate Truncated t Distribution
• europepmc-0.4.3 R Interface to the Europe PubMed Central RESTful Web Service
• fANCOVA-0.6-1 Nonparametric Analysis of Covariance
• faraway-1.0.9 Datasets and Functions for Books by Julian Faraway
• fastseg-1.52.0 fastseg - a fast segmentation algorithm
• fasttime-1.1-0 Fast Utility Function for Time Parsing and Conversion
• fda-6.2.0 Functional Data Analysis
• fds-1.8 Functional Data Sets
• fgsea-1.32.2 Fast Gene Set Enrichment Analysis
• filelock-1.0.3 Portable File Locking
• fit.models-0.64 Compare Fitted Models
• float-0.3-2 32-Bit Floats
• flowClust-3.44.0 Clustering for Flow Cytometry
• flowCore-2.18.0 flowCore: Basic structures for flow cytometry data
• flowStats-4.18.0 Statistical methods for the analysis of flow cytometry data
• flowViz-1.70.0 Visualization for flow cytometry
• flowWorkspace-4.18.0 Infrastructure for representing and interacting with gated and ungated cytometry data sets.
• forestplot-3.1.6 Advanced Forest Plot Using ‘grid’ Graphics
• forge-0.2.0 Casting Values into Shape
• fts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)
• gage-2.56.0 Generally Applicable Gene-set Enrichment for Pathway Analysis
• gcrma-2.78.0 Background Adjustment Using Sequence Information
• gdsfmt-1.42.1 R Interface to CoreArray Genomic Data Structure (GDS) Files
• geneLenDataBase 1.39.0 Package Not Found
• genefilter-1.88.0 genefilter: methods for filtering genes from high-throughput experiments
• geneplotter-1.84.0 Graphics related functions for Bioconductor
• ggVennDiagram-1.5.2 A ‘ggplot2’ Implement of Venn Diagram
• ggbio-1.54.0 Visualization tools for genomic data
• ggcyto-1.34.0 Visualize Cytometry data with ggplot
• ggdendro-0.2.0 Create Dendrograms and Tree Diagrams Using ‘ggplot2’
• ggnewscale-0.5.1 Multiple Fill and Colour Scales in ‘ggplot2’
• ggpointdensity-0.1.0 A Cross Between a 2D Density Plot and a Scatter Plot
• ggrastr-1.0.2 Rasterize Layers for ‘ggplot2’
• ggtangle-0.0.6 Draw Network with Data
• ggthemes-5.1.0 Extra Themes, Scales and Geoms for ‘ggplot2’
• ggtree-3.14.0 an R package for visualization of tree and annotation data
• glmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model
• graph-1.84.1 graph: A package to handle graph data structures
• gsignal-0.3-7 Signal Processing
• gson-0.1.0 Base Class and Methods for ‘gson’ Format
• gsubfn-0.7 Utilities for Strings and Function Arguments
• hapassoc-1.2-9 Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
• haplo.stats-1.9.7 Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
• hardhat-1.4.1 Construct Modeling Packages
• hdrcde-3.4 Highest Density Regions and Conditional Density Estimation
• hgu133plus2.db 3.13.0 Package Not Found
• hopach-2.66.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
• hypergate-0.8.5 Machine Learning of Hyperrectangular Gating Strategies for High-Dimensional Cytometry
• igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
• illuminaio-0.48.0 Parsing Illumina Microarray Output Files
• impute-1.80.0 impute: Imputation for microarray data
• inferference-1.0.2 Methods for Causal Inference with Interference
• interactiveDisplayBase-1.44.0 Base package for enabling powerful shiny web displays of Bioconductor objects
• invgamma-1.1 The Inverse Gamma Distribution
• iotools-0.3-5 I/O Tools for Streaming
• its-1.1.8 Irregular Time Series
• karyoploteR-1.32.0 Plot customizable linear genomes displaying arbitrary data
• keyring-1.3.2 Access the System Credential Store from R
• kin.cohort-0.7 Analysis of Kin-Cohort Studies
• knockoff-0.3.6 The Knockoff Filter for Controlled Variable Selection
• kyotil-2024.11-01 Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies
• latentnet-2.11.0 Latent Position and Cluster Models for Statistical Networks
• lgr-0.4.4 A Fully Featured Logging Framework
• limma-3.62.2 Linear Models for Microarray and Omics Data
• lintr-3.2.0 A ‘Linter’ for R Code
• lokern-1.1-12 Kernel Regression Smoothing with Local or Global Plug-in Bandwidth
• lpridge-1.1-0 Local Polynomial (Ridge) Regression
• lpsymphony-1.34.0 Symphony integer linear programming solver in R
• lumi-2.58.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
• maSigPro-1.78.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
• mapdata-2.3.1 Extra Map Databases
• marray-1.84.0 Exploratory analysis for two-color spotted microarray data
• metagenomeSeq-1.48.1 Statistical analysis for sparse high-throughput sequencing
• methylKit-1.32.1 DNA methylation analysis from high-throughput bisulfite sequencing results
• methylumi-2.52.0 Handle Illumina methylation data
• minfi-1.52.1 Analyze Illumina Infinium DNA methylation arrays
• mixOmics-6.30.0 Omics Data Integration Project
• mixsqp-0.3-54 Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions
• mlapi-0.1.1 Abstract Classes for Building ‘scikit-learn’ Like API
• modelenv-0.2.0 Provide Tools to Register Models for Use in ‘tidymodels’
• mondate-1.0 Keep Track of Dates in Terms of Months
• motifmatchr-1.28.0 Fast Motif Matching in R
• msa-1.38.0 Multiple Sequence Alignment
• msigdbr-7.5.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
• multtest-2.62.0 Resampling-based multiple hypothesis testing
• nanotime-0.3.11 Nanosecond-Resolution Time Support for R
• ncdfFlow-2.52.1 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
• networksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through Sequential Importance Sampling
• numbers-0.8-5 Number-Theoretic Functions
• nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
• odbc-1.6.0 Connect to ODBC Compatible Databases (using the DBI Interface)
• oligo-1.70.1 Preprocessing tools for oligonucleotide arrays
• oligoClasses-1.68.0 Classes for high-throughput arrays supported by oligo and crlmm
• openCyto-2.18.0 Hierarchical Gating Pipeline for flow cytometry data
• org.Hs.eg.db 3.19.1 Package Not Found
• org.Mm.eg.db 3.19.1 Package Not Found
• pack-0.1-1 Convert values to/from raw vectors
• parsnip-1.3.0 A Common API to Modeling and Analysis Functions
• partools-1.1.6 Tools for the ‘Parallel’ Package
• pathview-1.46.0 a tool set for pathway based data integration and visualization
• paws-0.8.0 Amazon Web Services Software Development Kit
• paws.analytics-0.8.0 ‘Amazon Web Services’ Analytics Services
• paws.application.integration-0.8.0 ‘Amazon Web Services’ Application Integration Services
• paws.common-0.8.2 Paws Low-Level Amazon Web Services API
• paws.compute-0.8.0 ‘Amazon Web Services’ Compute Services
• paws.cost.management-0.8.0 ‘Amazon Web Services’ Cost Management Services
• paws.customer.engagement-0.8.0 ‘Amazon Web Services’ Customer Engagement Services
• paws.database-0.8.0 ‘Amazon Web Services’ Database Services
• paws.developer.tools-0.8.0 ‘Amazon Web Services’ Developer Tools Services
• paws.end.user.computing-0.8.0 ‘Amazon Web Services’ End User Computing Services
• paws.machine.learning-0.8.0 ‘Amazon Web Services’ Machine Learning Services
• paws.management-0.8.0 ‘Amazon Web Services’ Management & Governance Services
• paws.networking-0.8.0 ‘Amazon Web Services’ Networking & Content Delivery Services
• paws.security.identity-0.8.0 ‘Amazon Web Services’ Security, Identity, & Compliance Services
• paws.storage-0.8.0 ‘Amazon Web Services’ Storage Services
• pbs-1.1 Periodic B Splines
• pcaMethods-1.98.0 A collection of PCA methods
• pdist-1.2.1 Partitioned Distance Function
• pedigree-1.4.2 Pedigree Functions
• pedigreemm-0.3-5 Pedigree-Based Mixed-Effects Models
• perm-1.0-0.4 Exact or Asymptotic Permutation Tests
• phyloseq-1.50.0 Handling and analysis of high-throughput microbiome census data
• poisbinom-1.0.1 A Faster Implementation of the Poisson-Binomial Distribution
• polyester-1.39.0 Simulate RNA-seq reads
• polyreg-0.8.0 Polynomial Regression
• poweRlaw-1.0.0 Analysis of Heavy Tailed Distributions
• premessa 0.3.4 Package Not Found
• preprocessCore-1.68.0 A collection of pre-processing functions
• psychotools-0.7-4 Psychometric Modeling Infrastructure
• pwalign-1.2.0 Perform pairwise sequence alignments
• qdapRegex-0.7.8 Regular Expression Removal, Extraction, and Replacement Tools
• qpdf-1.3.4 Split, Combine and Compress PDF Files
• qqconf-1.3.2 Creates Simultaneous Testing Bands for QQ-Plots
• qtl-1.70 Tools for Analyzing QTL Experiments
• quantoptr-0.1.3 Algorithms for Quantile- And Mean-Optimal Treatment Regimes
• quantsmooth-1.72.0 Quantile smoothing and genomic visualization of array data
• qvalue-2.38.0 Q-value estimation for false discovery rate control
• qvcalc-1.0.4 Quasi Variances for Factor Effects in Statistical Models
• r2d3-0.2.6 Interface to ‘D3’ Visualizations
• rGADEM-2.54.0 de novo motif discovery
• rainbow-3.8 Bagplots, Boxplots and Rainbow Plots for Functional Data
• rbenchmark-1.0.0 Benchmarking routine for R
• refGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from ‘Ensembl’ and ‘UCSC’ Genome Browsers
• refund-0.1-37 Regression with Functional Data
• regioneR-1.38.0 Association analysis of genomic regions based on permutation tests
• regress-1.3-21 Gaussian Linear Models with Linear Covariance Structure
• regtools-1.7.0 Regression and Classification Tools
• relations-0.6-15 Data Structures and Algorithms for Relations
• relevent-1.2-1 Relational Event Models
• repr-1.1.7 Serializable Representations
• restfulr-0.0.15 R Interface to RESTful Web Services
• rgenoud-5.9-0.11 R Version of GENetic Optimization Using Derivatives
• rhdf5-2.50.2 R Interface to HDF5
• rhdf5filters-1.18.1 HDF5 Compression Filters
• rjags-4-16 Bayesian Graphical Models using MCMC
• rje-1.12.1 Miscellaneous Useful Functions for Statistics
• rslurm-0.6.2 Submit R Calculations to a ‘Slurm’ Cluster
• rsparse-0.5.3 Statistical Learning on Sparse Matrices
• rstanarm-2.32.1 Bayesian Applied Regression Modeling via Stan
• rsvd-1.0.5 Randomized Singular Value Decomposition
• rtracklayer-1.66.0 R interface to genome annotation files and the UCSC genome browser
• rvcheck-0.2.1 R/Package Version Check
• rzmq-0.9.15 R Bindings for ‘ZeroMQ’
• samr-3.0 SAM: Significance Analysis of Microarrays
• scater-1.34.1 Single-Cell Analysis Toolkit for Gene Expression Data in R
• scattermore-1.2 Scatterplots with More Points
• schoolmath-0.4.2 Functions and Datasets for Math Used in School
• scidb-3.0.0 An R Interface to SciDB
• scrime-1.3.5 Analysis of High-Dimensional Categorical Data Such as SNP Data
• scuttle-1.16.0 Single-Cell RNA-Seq Analysis Utilities
• seqLogo-1.72.0 Sequence logos for DNA sequence alignments
• seqminer-9.7 Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
• sets-1.0-25 Sets, Generalized Sets, Customizable Sets and Intervals
• sfd-0.1.0 Space-Filling Design Library
• shinyBS-0.61.1 Twitter Bootstrap Components for Shiny
• shinyFiles-0.9.3 A Server-Side File System Viewer for Shiny
• shinyjqui-0.4.1 ‘jQuery UI’ Interactions and Effects for Shiny
• siggenes-1.80.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
• sitmo-2.0.2 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header Files
• snpStats-1.56.0 SnpMatrix and XSnpMatrix classes and methods
• sodium-1.4.0 A Modern and Easy-to-Use Crypto Library
• sparklyr-1.8.6 R Interface to Apache Spark
• sparseMatrixStats-1.18.0 Summary Statistics for Rows and Columns of Sparse Matrices
• sparsevctrs-0.3.0 Sparse Vectors for Use in Data Frames
• sqldf-0.4-11 Manipulate R Data Frames Using SQL
• squash-1.0.9 Color-Based Plots for Multivariate Visualization
• srvyr-1.3.0 ‘dplyr’-Like Syntax for Summary Statistics of Survey Data
• ssgraph-1.15 Bayesian Graph Structure Learning using Spike-and-Slab Priors
• sva-3.54.0 Surrogate Variable Analysis
• systemPipeR-2.12.0 systemPipeR: Workflow Environment for Data Analysis and Report Generation
• tables-0.9.31 Formula-Driven Table Generation
• tergmLite-2.6.1 Fast Simulation of Simple Temporal Exponential Random Graph Models
• text2vec-0.6.4 Modern Text Mining Framework for R
• tidyposterior-1.0.1 Bayesian Analysis to Compare Models using Resampling Statistics
• tilingArray-1.84.0 Transcript mapping with high-density oligonucleotide tiling arrays
• timeSeries-4041.111 Financial Time Series Objects (Rmetrics)
• tkWidgets-1.84.0 R based tk widgets
• treeio-1.30.0 Base Classes and Functions for Phylogenetic Tree Input and Output
• tune-1.3.0 Tidy Tuning Tools
• txdbmaker-1.2.1 Tools for making TxDb objects from genomic annotations
• udunits2-0.13.2.1 Udunits-2 Bindings for R
• universalmotif-1.24.2 Import, Modify, and Export Motifs with R
• uwot-0.2.3 The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction
• venn-1.12 Draw Venn Diagrams
• vimp-2.3.3 Perform Inference on Algorithm-Agnostic Variable Importance
• vsn-3.74.0 Variance stabilization and calibration for microarray data
• wavethresh-4.7.3 Wavelets Statistics and Transforms
• webp-1.3.0 A New Format for Lossless and Lossy Image Compression
• widgetTools-1.84.0 Creates an interactive tcltk widget
• workflows-1.2.0 Modeling Workflows
• workflowsets-1.1.0 Create a Collection of ‘tidymodels’ Workflows
• xCell 1.1.0 Package Not Found
• xmlparsedata-1.0.5 Parse Data of ‘R’ Code as an ‘XML’ Tree
• yardstick-1.3.2 Tidy Characterizations of Model Performance
• yulab.utils-0.2.0 Supporting Functions for Packages Maintained by ‘YuLab-SMU’
• zCompositions-1.5.0-4 Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
• zigg-0.0.2 Lightweight Interfaces to the ‘Ziggurat’ Pseudo Random Number Generator
• zlibbioc-1.52.0 An R packaged zlib-1.2.5

  Library List from dependent Modules

• ADGofTest-0.3 Anderson-Darling GoF test
• AICcmodavg-2.3-3 Model Selection and Multimodel Inference Based on (Q)AIC(c)
• ALDEx2-1.38.0 Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
• ALL 1.48.0 Package Not Found
• AMAPVox-2.2.1 LiDAR Data Voxelisation
• ANCOMBC-2.8.0 Microbiome differential abudance and correlation analyses with bias correction
• ATACseqQC-1.30.0 ATAC-seq Quality Control
• AUC-0.3.2 Threshold Independent Performance Measures for Probabilistic Classifiers
• AUCell-1.28.0 AUCell: Analysis of ‘gene set’ activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
• AgiMicroRna-2.56.0 Processing and Differential Expression Analysis of Agilent microRNA chips
• AlgDesign-1.2.1.1 Algorithmic Experimental Design
• AnnotationDbi-1.68.0 Manipulation of SQLite-based annotations in Bioconductor
• AnnotationFilter-1.30.0 Facilities for Filtering Bioconductor Annotation Resources
• AnnotationForge-1.48.0 Tools for building SQLite-based annotation data packages
• AnnotationHub-3.14.0 Client to access AnnotationHub resources
• BB-2019.10-1 Solving and Optimizing Large-Scale Nonlinear Systems
• BBmisc-1.13 Miscellaneous Helper Functions for B. Bischl
• BCEE-1.3.2 The Bayesian Causal Effect Estimation Algorithm
• BDgraph-2.73 Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
• BH-1.84.0-0 Boost C++ Header Files
• BIEN-1.2.6 Tools for Accessing the Botanical Information and Ecology Network Database
• BIGL-1.9.3 Biochemically Intuitive Generalized Loewe Model
• BMA-3.18.19 Bayesian Model Averaging
• BSgenome-1.74.0 Software infrastructure for efficient representation of full genomes and their SNPs
• BSgenome.Cfamiliaris.UCSC.canFam3 1.4.0 Package Not Found
• BSgenome.Hsapiens.UCSC.hg19 1.4.3 Package Not Found
• BSgenome.Hsapiens.UCSC.hg38 1.4.5 Package Not Found
• BSgenome.Mmusculus.UCSC.mm10 1.4.3 Package Not Found
• BatchJobs-1.9 Batch Computing with R
• BayesLogit-2.1 PolyaGamma Sampling
• BayesPen-1.0 Bayesian Penalized Credible Regions
• BayesianTools-0.1.8 General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
• BiasedUrn-2.0.12 Biased Urn Model Distributions
• Biobase-2.66.0 Biobase: Base functions for Bioconductor
• BiocBaseUtils-1.8.0 General utility functions for developing Bioconductor packages
• BiocFileCache-2.14.0 Manage Files Across Sessions
• BiocGenerics-0.52.0 S4 generic functions used in Bioconductor
• BiocIO-1.16.0 Standard Input and Output for Bioconductor Packages
• BiocManager-1.30.25 Access the Bioconductor Project Package Repository
• BiocNeighbors-2.0.0 Nearest Neighbor Detection for Bioconductor Packages
• BiocParallel-1.40.0 Bioconductor facilities for parallel evaluation
• BiocSingular-1.22.0 Singular Value Decomposition for Bioconductor Packages
• BiocStyle-2.34.0 Standard styles for vignettes and other Bioconductor documents
• BiocVersion-3.20.0 Set the appropriate version of Bioconductor packages
• Biostrings-2.74.0 Efficient manipulation of biological strings
• Boruta-8.0.0 Wrapper Algorithm for All Relevant Feature Selection
• Brobdingnag-1.2-9 Very Large Numbers in R
• CAGEfightR-1.26.0 Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
• CAGEr-2.12.0 Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
• CAMERA-1.62.0 Collection of annotation related methods for mass spectrometry data
• CBPS-0.23 Covariate Balancing Propensity Score
• CGHbase-1.66.0 CGHbase: Base functions and classes for arrayCGH data analysis.
• CGHcall-2.68.0 Calling aberrations for array CGH tumor profiles.
• CNEr-1.42.0 CNE Detection and Visualization
• CVST-0.2-3 Fast Cross-Validation via Sequential Testing
• CVXR-1.0-15 Disciplined Convex Optimization
• Cairo-1.6-2 R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output
• Category-2.72.0 Category Analysis
• ChIPpeakAnno-3.40.0 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
• ChIPseeker-1.42.0 ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
• ComICS-1.0.4 Computational Methods for Immune Cell-Type Subsets
• CompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal Variables
• ComplexHeatmap-2.22.0 Make Complex Heatmaps
• ComplexUpset-1.3.3 Create Complex UpSet Plots Using ‘ggplot2’ Components
• ConsRank-2.1.4 Compute the Median Ranking(s) According to the Kemeny’s Axiomatic Approach
• ConsensusClusterPlus-1.70.0 ConsensusClusterPlus
• CovSel-1.2.1 Model-Free Covariate Selection
• CytoML-2.18.0 A GatingML Interface for Cross Platform Cytometry Data Sharing
• DBI-1.2.3 R Database Interface
• DECIPHER-3.2.0 Tools for curating, analyzing, and manipulating biological sequences
• DEGseq-1.60.0 Identify Differentially Expressed Genes from RNA-seq data
• DESeq2-1.46.0 Differential gene expression analysis based on the negative binomial distribution
• DEoptim-2.2-8 Global Optimization by Differential Evolution
• DEoptimR-1.1-3-1 Differential Evolution Optimization in Pure R
• DHARMa-0.4.7 Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
• DMCfun-4.0.1 Diffusion Model of Conflict (DMC) in Reaction Time Tasks
• DNABarcodes-1.36.0 A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
• DNAcopy-1.80.0 DNA Copy Number Data Analysis
• DO.db 2.9 Package Not Found
• DOSE-4.0.0 Disease Ontology Semantic and Enrichment analysis
• DRIMSeq-1.34.0 Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
• DRR-0.0.4 Dimensionality Reduction via Regression
• DSS-2.54.0 Dispersion shrinkage for sequencing data
• DT-0.33 A Wrapper of the JavaScript Library ‘DataTables’
• DTRreg-2.2 DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
• DataCombine-0.2.21 Tools for Easily Combining and Cleaning Data Sets
• DeconRNASeq-1.48.0 Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
• DelayedArray-0.32.0 A unified framework for working transparently with on-disk and in-memory array-like datasets
• DelayedMatrixStats-1.28.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
• DepthProc-2.1.5 Statistical Depth Functions for Multivariate Analysis
• Deriv-4.1.6 Symbolic Differentiation
• DescTools-0.99.58 Tools for Descriptive Statistics
• DiagrammeR-1.0.11 Graph/Network Visualization
• DiceKriging-1.6.0 Kriging Methods for Computer Experiments
• DirichletMultinomial-1.48.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
• DiscriMiner-0.1-29 Tools of the Trade for Discriminant Analysis
• DistributionUtils-0.6-1 Distribution Utilities
• DropletUtils-1.26.0 Utilities for Handling Single-Cell Droplet Data
• DynDoc-1.84.0 Dynamic document tools
• EBImage-4.48.0 Image processing and analysis toolbox for R
• ECOSolveR-0.5.5 Embedded Conic Solver in R
• ENMeval-2.0.4 Automated Tuning and Evaluations of Ecological Niche Models
• EValue-4.1.3 Sensitivity Analyses for Unmeasured Confounding and Other Biases in Observational Studies and Meta-Analyses
• EasyABC-1.5.2 Efficient Approximate Bayesian Computation Sampling Schemes
• EnsDb.Hsapiens.v75 2.99.0 Package Not Found
• EnsDb.Hsapiens.v79 2.99.0 Package Not Found
• EnsDb.Hsapiens.v86 2.99.0 Package Not Found
• EnvStats-3.0.0 Package for Environmental Statistics, Including US EPA Guidance
• ExPosition-2.8.23 Exploratory Analysis with the Singular Value Decomposition
• Exact-3.3 Unconditional Exact Test
• ExperimentHub-2.14.0 Client to access ExperimentHub resources
• FDb.InfiniumMethylation.hg19 2.2.0 Package Not Found
• FKSUM-1.0.1 Fast Kernel Sums
• FME-1.3.6.3 A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis
• FNN-1.1.4.1 Fast Nearest Neighbor Search Algorithms and Applications
• FRASER-2.2.0 Find RAre Splicing Events in RNA-Seq Data
• FactoMineR-2.11 Multivariate Exploratory Data Analysis and Data Mining
• FactorCopula-0.9.3 Factor, Bi-Factor, Second-Order and Factor Tree Copula Models
• FlowSOM-2.14.0 Using self-organizing maps for visualization and interpretation of cytometry data
• FlowSorted.Blood.EPIC 2.10.0 Package Not Found
• FlowSorted.CordBloodCombined.450k 1.22.0 Package Not Found
• Formula-1.2-5 Extended Model Formulas
• GENESIS-2.36.0 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
• GENIE3-1.28.0 GEne Network Inference with Ensemble of trees
• GEOmap-2.5-11 Topographic and Geologic Mapping
• GEOquery-2.74.0 Get data from NCBI Gene Expression Omnibus (GEO)
• GGally-2.2.1 Extension to ‘ggplot2’
• GJRM-0.2-6.7 Generalised Joint Regression Modelling
• GLAD-2.70.0 Gain and Loss Analysis of DNA
• GO.db 3.20.0 Package Not Found
• GOSemSim-2.32.0 GO-terms Semantic Similarity Measures
• GOstats-2.72.0 Tools for manipulating GO and microarrays
• GPArotation-2024.3-1 Gradient Projection Factor Rotation
• GSA-1.03.3 Gene Set Analysis
• GSEABase-1.68.0 Gene set enrichment data structures and methods
• GSVA-2.0.1 Gene Set Variation Analysis for Microarray and RNA-Seq Data
• GUTS-1.2.5 Fast Calculation of the Likelihood of a Stochastic Survival Model
• GWASExactHW-1.2 Exact Hardy-Weinburg Testing for Genome Wide Association Studies
• GWASTools-1.52.0 Tools for Genome Wide Association Studies
• GenSA-1.1.14.1 R Functions for Generalized Simulated Annealing
• GeneNet-1.2.16 Modeling and Inferring Gene Networks
• GenomeInfoDb-1.42.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
• GenomeInfoDbData 1.2.13 Package Not Found
• GenomicAlignments-1.42.0 Representation and manipulation of short genomic alignments
• GenomicFeatures-1.58.0 Query the gene models of a given organism/assembly
• GenomicFiles-1.42.0 Distributed computing by file or by range
• GenomicInteractions-1.40.0 Utilities for handling genomic interaction data
• GenomicRanges-1.58.0 Representation and manipulation of genomic intervals
• GenomicScores-2.18.0 Infrastructure to work with genomewide position-specific scores
• GetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable Interpolation
• GillespieSSA-0.6.2 Gillespie’s Stochastic Simulation Algorithm (SSA)
• Glimma-2.16.0 Interactive visualizations for gene expression analysis
• GlobalAncova-4.24.0 Global test for groups of variables via model comparisons
• GlobalOptions-0.1.2 Generate Functions to Get or Set Global Options
• Gviz-1.50.0 Plotting data and annotation information along genomic coordinates
• GxEScanR-2.0.2 Run GWAS/GWEIS Scans Using Binary Dosage Files
• HDF5Array-1.34.0 HDF5 datasets as array-like objects in R
• HDO.db 1.0.0 Package Not Found
• HGNChelper-0.8.15 Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols
• HMMcopy-1.48.0 Copy number prediction with correction for GC and mappability bias for HTS data
• HWxtest-1.1.9 Exact Tests for Hardy-Weinberg Proportions
• HiCBricks-1.24.0 Framework for Storing and Accessing Hi-C Data Through HDF Files
• HiCcompare-1.28.0 HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
• HiddenMarkov-1.8-13 Hidden Markov Models
• Hmisc-5.2-0 Harrell Miscellaneous
• Hmsc-3.0-13 Hierarchical Model of Species Communities
• Homo.sapiens 1.3.1 Package Not Found
• IDPmisc-1.1.21 ‘Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)’
• IHW-1.34.0 Independent Hypothesis Weighting
• IRanges-2.40.0 Foundation of integer range manipulation in Bioconductor
• ISOcodes-2024.02.12 Selected ISO Codes
• ISOweek-0.6-2 Week of the year and weekday according to ISO 8601
• IlluminaHumanMethylation450kanno.ilmn12.hg19 0.6.1 Package Not Found
• IlluminaHumanMethylation450kmanifest 0.4.0 Package Not Found
• IlluminaHumanMethylationEPICanno.ilm10b2.hg19 0.6.0 Package Not Found
• IlluminaHumanMethylationEPICanno.ilm10b4.hg19 0.6.0 Package Not Found
• IlluminaHumanMethylationEPICmanifest 0.3.0 Package Not Found
• IlluminaHumanMethylationEPICv2anno.20a1.hg38 1.0.0 Package Not Found
• IlluminaHumanMethylationEPICv2manifest 1.0.0 Package Not Found
• InteractionSet-1.34.0 Base Classes for Storing Genomic Interaction Data
• Iso-0.0-21 Functions to Perform Isotonic Regression
• JADE-2.0-4 Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria
• JASPAR2020 0.99.10 Package Not Found
• JBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J. Buttlar
• KEGGREST-1.46.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
• KEGGgraph-1.66.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
• KODAMA-2.4.1 Knowledge Discovery by Accuracy Maximization
• KernSmooth-2.23-24 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
• LCFdata-2.0 Data sets for package “LMERConvenienceFunctions”
• LEA-3.18.0 LEA: an R package for Landscape and Ecological Association Studies
• LMERConvenienceFunctions-3.0 Model Selection and Post-Hoc Analysis for (G)LMER Models
• LaplacesDemon-16.1.6 Complete Environment for Bayesian Inference
• LearnBayes-2.15.1 Functions for Learning Bayesian Inference
• Lmoments-1.3-1 L-Moments and Quantile Mixtures
• M3Drop-1.32.0 Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
• MALDIquant-1.22.3 Quantitative Analysis of Mass Spectrometry Data
• MASS-7.3-61 Support Functions and Datasets for Venables and Ripley’s MASS
• MBA-0.1-2 Multilevel B-Spline Approximation
• MCMCpack-1.7-1 Markov Chain Monte Carlo (MCMC) Package
• MEDIPS-1.58.0 DNA IP-seq data analysis
• MESS-0.5.12 Miscellaneous Esoteric Statistical Scripts
• MIIVsem-0.5.8 Model Implied Instrumental Variable (MIIV) Estimation of Structural Equation Models
• MLInterfaces-1.86.0 Uniform interfaces to R machine learning procedures for data in Bioconductor containers
• MLmetrics-1.1.3 Machine Learning Evaluation Metrics
• MSnbase-2.32.0 Base Functions and Classes for Mass Spectrometry and Proteomics
• MSstats-4.14.0 Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
• MSstatsConvert-1.16.0 Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
• MSstatsLiP-1.12.0 LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
• MSstatsPTM-2.8.1 Statistical Characterization of Post-translational Modifications
• MSstatsTMT-2.14.1 Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
• MassSpecWavelet-1.72.0 Peak Detection for Mass Spectrometry data using wavelet-based algorithms
• MatchIt-4.6.0 Nonparametric Preprocessing for Parametric Causal Inference
• Matching-4.10-15 Multivariate and Propensity Score Matching with Balance Optimization
• Matrix-1.7-1 Sparse and Dense Matrix Classes and Methods
• MatrixGenerics-1.18.0 S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
• MatrixModels-0.5-3 Modelling with Sparse and Dense Matrices
• MetaUtility-2.1.2 Utility Functions for Conducting and Interpreting Meta-Analyses
• MetaboCoreUtils-1.14.0 Core Utils for Metabolomics Data
• MethylSeekR-1.46.0 Segmentation of Bis-seq data
• Mfuzz-2.66.0 Soft clustering of omics time series data
• ModelMetrics-1.2.2.2 Rapid Calculation of Model Metrics
• MonteCarlo-1.0.6 Automatic Parallelized Monte Carlo Simulations
• MotifDb-1.48.0 An Annotated Collection of Protein-DNA Binding Sequence Motifs
• MsCoreUtils-1.18.0 Core Utils for Mass Spectrometry Data
• MsExperiment-1.8.0 Infrastructure for Mass Spectrometry Experiments
• MsFeatures-1.14.0 Functionality for Mass Spectrometry Features
• MultiAssayExperiment-1.32.0 Software for the integration of multi-omics experiments in Bioconductor
• MultiDataSet-1.34.0 Implementation of MultiDataSet and ResultSet
• NADA-1.6-1.1 Nondetects and Data Analysis for Environmental Data
• NCmisc-1.2.0 Miscellaneous Functions for Creating Adaptive Functions and Scripts
• NISTunits-1.0.1 Fundamental Physical Constants and Unit Conversions from NIST
• NLP-0.3-2 Natural Language Processing Infrastructure
• NMF-0.28 Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
• NOISeq-2.50.0 Exploratory analysis and differential expression for RNA-seq data
• OUTRIDER-1.24.0 OUTRIDER - OUTlier in RNA-Seq fInDER
• OceanView-1.0.7 Visualisation of Oceanographic Data and Model Output
• OpenMx-2.21.13 Extended Structural Equation Modelling
• OrganismDbi-1.48.0 Software to enable the smooth interfacing of different database packages
• PCAmatchR-0.3.3 Match Cases to Controls Based on Genotype Principal Components
• PFAM.db 3.20.0 Package Not Found
• PKI-0.1-14 Public Key Infrastucture for R Based on the X.509 Standard
• PMA-1.2-4 Penalized Multivariate Analysis
• PRROC-1.3.1 Precision-Recall and ROC Curves for Weighted and Unweighted Data
• PSCBS-0.67.0 Analysis of Parent-Specific DNA Copy Numbers
• PSMatch-1.10.0 Handling and Managing Peptide Spectrum Matches
• PWEALL-1.3.0.1 Design and Monitoring of Survival Trials Accounting for Complex Situations
• ParamHelpers-1.14.1 Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning
• PearsonDS-1.3.1 Pearson Distribution System
• PermAlgo-1.2 Permutational Algorithm to Simulate Survival Data
• PoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log linear model
• Polychrome-1.5.1 Qualitative Palettes with Many Colors
• PresenceAbsence-1.1.11 Presence-Absence Model Evaluation
• ProtGenerics-1.38.0 Generic infrastructure for Bioconductor mass spectrometry packages
• Publish-2023.01.17 Format Output of Various Routines in a Suitable Way for Reports and Publication
• PureCN-2.12.0 Copy number calling and SNV classification using targeted short read sequencing
• QDNAseq-1.42.0 Quantitative DNA Sequencing for Chromosomal Aberrations
• QFeatures-1.16.0 Quantitative features for mass spectrometry data
• QuickJSR-1.4.0 Interface for the ‘QuickJS’ Lightweight ‘JavaScript’ Engine
• R.cache-0.16.0 Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations
• R.devices-2.17.2 Unified Handling of Graphics Devices
• R.filesets-2.15.1 Easy Handling of and Access to Files Organized in Structured Directories
• R.huge-0.10.1 Methods for Accessing Huge Amounts of Data [deprecated]
• R.matlab-3.7.0 Read and Write MAT Files and Call MATLAB from Within R
• R.methodsS3-1.8.2 S3 Methods Simplified
• R.oo-1.27.0 R Object-Oriented Programming with or without References
• R.rsp-0.46.0 Dynamic Generation of Scientific Reports
• R.utils-2.12.3 Various Programming Utilities
• R2WinBUGS-2.1-22.1 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
• R6-2.5.1 Encapsulated Classes with Reference Semantics
• RANN-2.6.2 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric
• RBGL-1.82.0 An interface to the BOOST graph library
• RBesT-1.7-4 R Bayesian Evidence Synthesis Tools
• RCAL-2.0 Regularized Calibrated Estimation
• RCircos-1.2.2 Circos 2D Track Plot
• RColorBrewer-1.1-3 ColorBrewer Palettes
• RCurl-1.98-1.16 General Network (HTTP/FTP/…) Client Interface for R
• RFOC-3.4-10 Graphics for Spherical Distributions and Earthquake Focal Mechanisms
• RGCCA-3.0.3 Regularized and Sparse Generalized Canonical Correlation Analysis for Multiblock Data
• RInside-0.2.18 C++ Classes to Embed R in C++ (and C) Applications
• RItools-0.3-4 Randomization Inference Tools
• RJSONIO-1.3-1.9 Serialize R Objects to JSON, JavaScript Object Notation
• RMTstat-0.3.1 Distributions, Statistics and Tests Derived from Random Matrix Theory
• RNASeqPower-1.46.0 Sample size for RNAseq studies
• RNeXML-2.4.11 Semantically Rich I/O for the ‘NeXML’ Format
• RNifti-1.7.0 Fast R and C++ Access to NIfTI Images
• ROC-1.82.0 utilities for ROC, with microarray focus
• ROCR-1.0-11 Visualizing the Performance of Scoring Classifiers
• ROI-1.0-1 R Optimization Infrastructure
• ROI.plugin.glpk-1.0-0 ‘ROI’ Plug-in ‘GLPK’
• ROntoTools-2.34.0 R Onto-Tools suite
• RPMG-2.2-7 Graphical User Interface (GUI) for Interactive R Analysis Sessions
• RPMM-1.25 Recursively Partitioned Mixture Model
• RPostgreSQL-0.7-7 R Interface to the ‘PostgreSQL’ Database System
• RProtoBufLib-2.18.0 C++ headers and static libraries of Protocol buffers
• RPushbullet-0.3.4 R Interface to the Pushbullet Messaging Service
• RSEIS-4.2-4 Seismic Time Series Analysis Tools
• RSNNS-0.4-17 Neural Networks using the Stuttgart Neural Network Simulator (SNNS)
• RSQLite-2.3.8 SQLite Interface for R
• RSpectra-0.16-2 Solvers for Large-Scale Eigenvalue and SVD Problems
• RUnit-0.4.33 R Unit Test Framework
• RWeka-0.4-46 R/Weka Interface
• RWekajars-3.9.3-2 R/Weka Interface Jars
• Rborist-0.3-7 Extensible, Parallelizable Implementation of the Random Forest Algorithm
• Rcgmin-2022-4.30 Conjugate Gradient Minimization of Nonlinear Functions with Box Constraints
• RcisTarget-1.26.0 RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions
• Rcpp-1.0.13-1 Seamless R and C++ Integration
• RcppAnnoy-0.0.22 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest Neighbors
• RcppArmadillo-14.2.0-1 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra Library
• RcppEigen-0.3.4.0.2 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra Library
• RcppGSL-0.3.13 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and Matrices
• RcppHNSW-0.6.0 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest Neighbors
• RcppML-0.3.7 Rcpp Machine Learning Library
• RcppParallel-5.1.9 Parallel Programming Tools for ‘Rcpp’
• RcppProgress-0.4.2 An Interruptible Progress Bar with OpenMP Support for C++ in R Packages
• RcppRoll-0.3.1 Efficient Rolling / Windowed Operations
• RcppTOML-0.2.2 ‘Rcpp’ Bindings to Parser for “Tom’s Obvious Markup Language”
• RcppThread-2.1.7 R-Friendly Threading in C++
• RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG Implementations
• Rdpack-2.6.2 Update and Manipulate Rd Documentation Objects
• ReactomePA-1.50.0 Reactome Pathway Analysis
• RefFreeEWAS-2.2 EWAS using Reference-Free DNA Methylation Mixture Deconvolution
• Repitools-1.52.0 Epigenomic tools
• ReportingTools-2.46.0 Tools for making reports in various formats
• ResidualMatrix-1.16.0 Creating a DelayedMatrix of Regression Residuals
• Rfast-2.1.0 A Collection of Efficient and Extremely Fast R Functions
• Rglpk-0.6-5.1 R/GNU Linear Programming Kit Interface
• Rgraphviz-2.50.0 Provides plotting capabilities for R graph objects
• Rhdf5lib-1.28.0 hdf5 library as an R package
• RhpcBLASctl-0.23-42 Control the Number of Threads on ‘BLAS’
• Rhtslib-3.2.0 HTSlib high-throughput sequencing library as an R package
• Rmpfr-1.0-0 Interface R to MPFR - Multiple Precision Floating-Point Reliable
• RnBeads-2.24.0 RnBeads
• RnBeads.hg19 1.38.0 Package Not Found
• RnBeads.hg38 1.38.0 Package Not Found
• RnBeads.mm10 2.14.0 Package Not Found
• RnBeads.mm9 1.38.0 Package Not Found
• RnBeads.rn5 1.38.0 Package Not Found
• Rook-1.2 HTTP Web Server for R
• Rsamtools-2.22.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
• Rserve-1.8-13 Versatile R Server
• Rsolnp-1.16 General Non-Linear Optimization
• Rssa-1.1 A Collection of Methods for Singular Spectrum Analysis
• Rsubread-2.20.0 Mapping, quantification and variant analysis of sequencing data
• Rtsne-0.17 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
• Rttf2pt1-1.3.12 ‘ttf2pt1’ Program
• Rvmmin-2018-4.17.1 Variable Metric Nonlinear Function Minimization
• Rwave-2.6-5 Time-Frequency Analysis of 1-D Signals
• S4Arrays-1.6.0 Foundation of array-like containers in Bioconductor
• S4Vectors-0.44.0 Foundation of vector-like and list-like containers in Bioconductor
• SBdecomp-1.2 Estimation of the Proportion of SB Explained by Confounders
• SC3-1.34.0 Single-Cell Consensus Clustering
• SCANVIS-1.20.0 SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
• SDMTools-1.1-221.2 Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises
• SKAT-2.2.5 SNP-Set (Sequence) Kernel Association Test
• SMVar-1.3.4 Structural Model for Variances
• SNFtool-2.3.1 Similarity Network Fusion
• SNPRelate-1.40.0 Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
• SOAR-0.99-11 Memory management in R by delayed assignments
• SPAtest-3.1.2 Score Test and Meta-Analysis Based on Saddlepoint Approximation
• SPIA-2.58.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
• SPOTlight-1.10.0 SPOTlight: Spatial Transcriptomics Deconvolution
• SQUAREM-2021.1 Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms
• SamSPECTRAL-1.60.0 Identifies cell population in flow cytometry data
• ScaledMatrix-1.14.0 Creating a DelayedMatrix of Scaled and Centered Values
• SeqArray-1.46.0 Data Management of Large-Scale Whole-Genome Sequence Variant Calls
• SeqVarTools-1.44.0 Tools for variant data
• Seurat-5.1.0 Tools for Single Cell Genomics
• SeuratObject-5.0.2 Data Structures for Single Cell Data
• ShortRead-1.64.0 FASTQ input and manipulation
• Signac-1.14.0 Analysis of Single-Cell Chromatin Data
• SignifReg-4.3 Consistent Significance Controlled Variable Selection in Generalized Linear Regression
• SimBu-1.8.0 Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
• SimDesign-2.17.1 Structure for Organizing Monte Carlo Simulation Designs
• SimSeq-1.4.0 Nonparametric Simulation of RNA-Seq Data
• SingleCellExperiment-1.28.1 S4 Classes for Single Cell Data
• SingleR-2.8.0 Reference-Based Single-Cell RNA-Seq Annotation
• SnowballC-0.7.1 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 Library
• SparseArray-1.6.0 High-performance sparse data representation and manipulation in R
• SparseM-1.84-2 Sparse Linear Algebra
• SpatialExperiment-1.16.0 S4 Class for Spatially Resolved -omics Data
• Spectra-1.16.0 Spectra Infrastructure for Mass Spectrometry Data
• StanHeaders-2.32.10 C++ Header Files for Stan
• StatMatch-1.4.2 Statistical Matching or Data Fusion
• SummarizedExperiment-1.36.0 A container (S4 class) for matrix-like assays
• SuperLearner-2.0-29 Super Learner Prediction
• SuppDists-1.1-9.8 Supplementary Distributions
• TFBSTools-1.44.0 Software Package for Transcription Factor Binding Site (TFBS) Analysis
• TFMPvalue-0.0.9 Efficient and Accurate P-Value Computation for Position Weight Matrices
• TFisher-0.2.0 Optimal Thresholding Fisher’s P-Value Combination Method
• TH.data-1.1-2 TH’s Data Archive
• TMB-1.9.15 Template Model Builder: A General Random Effect Tool Inspired by ‘ADMB’
• TSP-1.2-4 Traveling Salesperson Problem (TSP)
• TTR-0.24.4 Technical Trading Rules
• TailRank-3.2.2 The Tail-Rank Statistic
• TeachingDemos-2.13 Demonstrations for Teaching and Learning
• TraMineR-2.2-10 Trajectory Miner: a Sequence Analysis Toolkit
• TrajectoryUtils-1.14.0 Single-Cell Trajectory Analysis Utilities
• TreeSummarizedExperiment-2.14.0 TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
• TruncatedNormal-2.3 Truncated Multivariate Normal and Student Distributions
• TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2 Package Not Found
• TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0 Package Not Found
• UCSC.utils-1.2.0 Low-level utilities to retrieve data from the UCSC Genome Browser
• UCell-2.10.1 Rank-based signature enrichment analysis for single-cell data
• UpSetR-1.4.0 A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
• V8-6.0.0 Embedded JavaScript and WebAssembly Engine for R
• VGAM-1.1-12 Vector Generalized Linear and Additive Models
• VIM-6.2.2 Visualization and Imputation of Missing Values
• VSURF-1.2.0 Variable Selection Using Random Forests
• VariantAnnotation-1.52.0 Annotation of Genetic Variants
• VennDiagram-1.7.3 Generate High-Resolution Venn and Euler Plots
• VineCopula-2.5.1 Statistical Inference of Vine Copulas
• WGCNA-1.73 Weighted Correlation Network Analysis
• WeightSVM-1.7-16 Subject Weighted Support Vector Machines
• WikidataQueryServiceR-1.0.0 API Client Library for ‘Wikidata Query Service’
• WikidataR-2.3.3 Read-Write API Client Library for Wikidata
• WikipediR-1.7.1 A MediaWiki API Wrapper
• Wrench-1.24.0 Wrench normalization for sparse count data
• WriteXLS-6.7.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS) and Excel 2007 (XLSX) Files
• XBRL-0.99.19.1 Extraction of Business Financial Information from ‘XBRL’ Documents
• XML-3.99-0.17 Tools for Parsing and Generating XML Within R and S-Plus
• XVector-0.46.0 Foundation of external vector representation and manipulation in Bioconductor
• abc-2.2.1 Tools for Approximate Bayesian Computation (ABC)
• abc.data-1.1 Data Only: Tools for Approximate Bayesian Computation (ABC)
• abe-3.0.1 Augmented Backward Elimination
• abind-1.4-8 Combine Multidimensional Arrays
• acepack-1.4.2 ACE and AVAS for Selecting Multiple Regression Transformations
• adabag-5.0 Applies Multiclass AdaBoost.M1, SAMME and Bagging
• ade4-1.7-22 Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
• admisc-0.36 Adrian Dusa’s Miscellaneous
• affxparser-1.78.0 Affymetrix File Parsing SDK
• affy-1.84.0 Methods for Affymetrix Oligonucleotide Arrays
• affycoretools-1.78.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
• affyio-1.76.0 Tools for parsing Affymetrix data files
• aggregation-1.0.1 p-Value Aggregation Methods
• agricolae-1.3-7 Statistical Procedures for Agricultural Research
• akima-0.6-3.4 Interpolation of Irregularly and Regularly Spaced Data
• alabama-2023.1.0 Constrained Nonlinear Optimization
• alluvial-0.1-2 Alluvial Diagrams
• animation-2.7 A Gallery of Animations in Statistics and Utilities to Create Animations
• annaffy-1.78.0 Annotation tools for Affymetrix biological metadata
• annotate-1.84.0 Annotation for microarrays
• anytime-0.3.9 Anything to ‘POSIXct’ or ‘Date’ Converter
• aod-1.3.3 Analysis of Overdispersed Data
• apcluster-1.4.13 Affinity Propagation Clustering
• ape-5.8 Analyses of Phylogenetics and Evolution
• aplot-0.2.3 Decorate a ‘ggplot’ with Associated Information
• argparse-2.2.4 Command Line Optional and Positional Argument Parser
• aricode-1.0.3 Efficient Computations of Standard Clustering Comparison Measures
• arm-1.14-4 Data Analysis Using Regression and Multilevel/Hierarchical Models
• aroma.affymetrix-3.2.2 Analysis of Large Affymetrix Microarray Data Sets
• aroma.apd-0.7.0 A Probe-Level Data File Format Used by ‘aroma.affymetrix’ [deprecated]
• aroma.core-3.3.1 Core Methods and Classes Used by ‘aroma.*’ Packages Part of the Aroma Framework
• aroma.light-3.36.0 Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
• arrayhelpers-1.1-0 Convenience Functions for Arrays
• ash-1.0-15 David Scott’s ASH Routines
• askpass-1.2.1 Password Entry Utilities for R, Git, and SSH
• asnipe-1.1.17 Animal Social Network Inference and Permutations for Ecologists
• assertive-0.3-6 Readable Check Functions to Ensure Code Integrity
• assertive.base-0.0-9 A Lightweight Core of the ‘assertive’ Package
• assertive.code-0.0-4 Assertions to Check Properties of Code
• assertive.data-0.0-3 Assertions to Check Properties of Data
• assertive.data.uk-0.0-2 Assertions to Check Properties of Strings
• assertive.data.us-0.0-2 Assertions to Check Properties of Strings
• assertive.datetimes-0.0-3 Assertions to Check Properties of Dates and Times
• assertive.files-0.0-2 Assertions to Check Properties of Files
• assertive.matrices-0.0-2 Assertions to Check Properties of Matrices
• assertive.models-0.0-2 Assertions to Check Properties of Models
• assertive.numbers-0.0-2 Assertions to Check Properties of Numbers
• assertive.properties-0.0-5 Assertions to Check Properties of Variables
• assertive.reflection-0.0-5 Assertions for Checking the State of R
• assertive.sets-0.0-3 Assertions to Check Properties of Sets
• assertive.strings-0.0-3 Assertions to Check Properties of Strings
• assertive.types-0.0-3 Assertions to Check Types of Variables
• assertthat-0.2.1 Easy Pre and Post Assertions
• assorthead-1.0.0 Assorted Header-Only C++ Libraries
• audio-0.1-11 Audio Interface for R
• aws-2.5-6 Adaptive Weights Smoothing
• aws.s3-0.3.21 ‘AWS S3’ Client Package
• aws.signature-0.6.0 Amazon Web Services Request Signatures
• awsMethods-1.1-1 Class and Methods Definitions for Packages ‘aws’, ‘adimpro’, ‘fmri’, ‘dwi’
• babelgene-22.9 Gene Orthologs for Model Organisms in a Tidy Data Format
• backports-1.5.0 Reimplementations of Functions Introduced Since R-3.0.0
• bacr-1.0.1 Bayesian Adjustment for Confounding
• ballgown-2.38.0 Flexible, isoform-level differential expression analysis
• bartMachine-1.3.4.1 Bayesian Additive Regression Trees
• bartMachineJARs-1.2.1 bartMachine JARs
• base built in
• base64-2.0.2 Base64 Encoder and Decoder
• base64enc-0.1-3 Tools for base64 encoding
• basilisk-1.18.0 Freezing Python Dependencies Inside Bioconductor Packages
• basilisk.utils-1.18.0 Basilisk Installation Utilities
• batchelor-1.22.0 Single-Cell Batch Correction Methods
• batchmeans-1.0-4 Consistent Batch Means Estimation of Monte Carlo Standard Errors
• baySeq-2.40.0 Empirical Bayesian analysis of patterns of differential expression in count data
• bayesm-3.1-6 Bayesian Inference for Marketing/Micro-Econometrics
• bayesplot-1.11.1 Plotting for Bayesian Models
• bayestestR-0.15.0 Understand and Describe Bayesian Models and Posterior Distributions
• bbmle-1.0.25.1 Tools for General Maximum Likelihood Estimation
• bdsmatrix-1.3-7 Routines for Block Diagonal Symmetric Matrices
• beachmat-2.22.0 Compiling Bioconductor to Handle Each Matrix Type
• beanplot-1.3.1 Visualization via Beanplots (Like Boxplot/Stripchart/Violin Plot)
• beepr-2.0 Easily Play Notification Sounds on any Platform
• beeswarm-0.4.0 The Bee Swarm Plot, an Alternative to Stripchart
• berryFunctions-1.22.5 Function Collection Related to Plotting and Hydrology
• betareg-3.2-1 Beta Regression
• bibtex-0.5.1 Bibtex Parser
• bigD-0.3.0 Flexibly Format Dates and Times to a Given Locale
• bigmemory-4.6.4 Manage Massive Matrices with Shared Memory and Memory-Mapped Files
• bigmemory.sri-0.1.8 A Shared Resource Interface for Bigmemory Project Packages
• bindr-0.1.2 Parametrized Active Bindings
• bindrcpp-0.2.3 An ‘Rcpp’ Interface to Active Bindings
• bio3d-2.4-5 Biological Structure Analysis
• biom-0.3.12 An interface package (beta) for the BIOM file format.
• biomaRt-2.62.0 Interface to BioMart databases (i.e. Ensembl)
• biomformat-1.34.0 An interface package for the BIOM file format
• biomod2-4.2-5-2 Ensemble Platform for Species Distribution Modeling
• biovizBase-1.54.0 Basic graphic utilities for visualization of genomic data.
• bit-4.5.0 Classes and Methods for Fast Memory-Efficient Boolean Selections
• bit64-4.5.2 A S3 Class for Vectors of 64bit Integers
• bitops-1.0-9 Bitwise Operations
• blavaan-0.5-6 Bayesian Latent Variable Analysis
• blme-1.0-6 Bayesian Linear Mixed-Effects Models
• blob-1.2.4 A Simple S3 Class for Representing Vectors of Binary Data (‘BLOBS’)
• bluster-1.16.0 Clustering Algorithms for Bioconductor
• bmp-0.3 Read Windows Bitmap (BMP) Images
• bnlearn-5.0.1 Bayesian Network Structure Learning, Parameter Learning and Inference
• bold-1.3.0 Interface to Bold Systems API
• bookdown-0.41 Authoring Books and Technical Documents with R Markdown
• boot-1.3-31 Bootstrap Functions (Originally by Angelo Canty for S)
• bootstrap-2019.6 Functions for the Book “An Introduction to the Bootstrap”
• brew-1.0-10 Templating Framework for Report Generation
• brglm-0.7.2 Bias Reduction in Binomial-Response Generalized Linear Models
• bridgedist-0.1.3 An Implementation of the Bridge Distribution with Logit-Link as in Wang and Louis (2003)
• bridgesampling-1.1-2 Bridge Sampling for Marginal Likelihoods and Bayes Factors
• brio-1.1.5 Basic R Input Output
• brms-2.22.0 Bayesian Regression Models using ‘Stan’
• broom-1.0.7 Convert Statistical Objects into Tidy Tibbles
• broom.helpers-1.17.0 Helpers for Model Coefficients Tibbles
• broom.mixed-0.2.9.6 Tidying Methods for Mixed Models
• bslib-0.8.0 Custom ‘Bootstrap’ ‘Sass’ Themes for ‘shiny’ and ‘rmarkdown’
• bsseq-1.42.0 Analyze, manage and store whole-genome methylation data
• bst-0.3-24 Gradient Boosting
• bumphunter-1.48.0 Bump Hunter
• cNORM-3.4.0 Continuous Norming
• cSEM-0.5.0 Composite-Based Structural Equation Modeling
• ca-0.71.1 Simple, Multiple and Joint Correspondence Analysis
• caTools-1.18.3 Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
• cachem-1.1.0 Cache R Objects with Automatic Pruning
• calibrate-1.7.7 Calibration of Scatterplot and Biplot Axes
• callr-3.7.6 Call R from R
• car-3.1-3 Companion to Applied Regression
• carData-3.0-5 Companion to Applied Regression Data Sets
• cards-0.3.0 Analysis Results Data
• caret-6.0-94 Classification and Regression Training
• catlearn-1.0 Formal Psychological Models of Categorization and Learning
• ccdata 1.32.0 Package Not Found
• ccmap-1.32.0 Combination Connectivity Mapping
• celestial-1.4.6 Collection of Common Astronomical Conversion Routines and Functions
• cellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columns
• cgdsr-1.3.0 R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)
• cghFLasso-0.2-1 Detecting hot spot on CGH array data with fused lasso<U+000a>regression.
• changepoint-2.3 Methods for Changepoint Detection
• checkmate-2.3.2 Fast and Versatile Argument Checks
• chemometrics-1.4.4 Multivariate Statistical Analysis in Chemometrics
• chk-0.9.2 Check User-Supplied Function Arguments
• chkptstanr-0.1.1 Checkpoint MCMC Sampling with ‘Stan’
• chromVAR-1.28.0 Chromatin Variation Across Regions
• chron-2.3-61 Chronological Objects which Can Handle Dates and Times
• circlize-0.4.16 Circular Visualization
• circular-0.5-1 Circular Statistics
• clValid-0.7 Validation of Clustering Results
• class-7.3-22 Functions for Classification
• classInt-0.4-10 Choose Univariate Class Intervals
• cld2-1.2.5 Google’s Compact Language Detector 2
• cli-3.6.3 Helpers for Developing Command Line Interfaces
• clipr-0.8.0 Read and Write from the System Clipboard
• clisymbols-1.2.0 Unicode Symbols at the R Prompt
• clock-0.7.1 Date-Time Types and Tools
• clue-0.3-66 Cluster Ensembles
• cluster-2.1.6 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et al.
• clusterGeneration-1.3.8 Random Cluster Generation (with Specified Degree of Separation)
• clusterProfiler-4.14.3 A universal enrichment tool for interpreting omics data
• clusterRepro-0.9 Reproducibility of Gene Expression Clusters
• clustree-0.5.1 Visualise Clusterings at Different Resolutions
• cmna-1.0.5 Computational Methods for Numerical Analysis
• cmprsk-2.2-12 Subdistribution Analysis of Competing Risks
• cobalt-4.5.5 Covariate Balance Tables and Plots
• cobs-1.3-8 Constrained B-Splines (Sparse Matrix Based)
• coda-0.19-4.1 Output Analysis and Diagnostics for MCMC
• codetools-0.2-20 Code Analysis Tools for R
• coin-1.4-3 Conditional Inference Procedures in a Permutation Test Framework
• collapse-2.0.18 Advanced and Fast Data Transformation
• coloc-5.2.3 Colocalisation Tests of Two Genetic Traits
• colorRamps-2.3.4 Builds Color Tables
• colorspace-2.1-1 A Toolbox for Manipulating and Assessing Colors and Palettes
• colourpicker-1.3.0 A Colour Picker Tool for Shiny and for Selecting Colours in Plots
• combinat-0.0-8 combinatorics utilities
• commonmark-1.9.2 High Performance CommonMark and Github Markdown Rendering in R
• compiler built in
• compositions-2.0-8 Compositional Data Analysis
• conditionz-0.1.0 Control How Many Times Conditions are Thrown
• conflicted-1.2.0 An Alternative Conflict Resolution Strategy
• conquer-1.3.3 Convolution-Type Smoothed Quantile Regression
• contfrac-1.1-12 Continued Fractions
• conumee-1.40.0 Enhanced copy-number variation analysis using Illumina DNA methylation arrays
• copCAR-2.0-4 Fitting the copCAR Regression Model for Discrete Areal Data
• copula-1.1-4 Multivariate Dependence with Copulas
• corpcor-1.6.10 Efficient Estimation of Covariance and (Partial) Correlation
• corrplot-0.95 Visualization of a Correlation Matrix
• covr-3.6.4 Test Coverage for Packages
• covsim-1.1.0 VITA, IG and PLSIM Simulation for Given Covariance and Marginals
• cowplot-1.1.3 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’
• coxed-0.3.3 Duration-Based Quantities of Interest for the Cox Proportional Hazards Model
• coxme-2.2-22 Mixed Effects Cox Models
• cpp11-0.5.0 A C++11 Interface for R’s C Interface
• crayon-1.5.3 Colored Terminal Output
• credentials-2.0.2 Tools for Managing SSH and Git Credentials
• crfsuite-0.4.2 Conditional Random Fields for Labelling Sequential Data in Natural Language Processing
• crosstalk-1.2.1 Inter-Widget Interactivity for HTML Widgets
• crul-1.5.0 HTTP Client
• csSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarrays
• ctmle-0.1.2 Collaborative Targeted Maximum Likelihood Estimation
• cubature-2.1.1 Adaptive Multivariate Integration over Hypercubes
• cubelyr-1.0.2 A Data Cube ‘dplyr’ Backend
• cummeRbund-2.48.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
• curl-6.0.1 A Modern and Flexible Web Client for R
• cvAUC-1.1.4 Cross-Validated Area Under the ROC Curve Confidence Intervals
• cytolib-2.18.0 C++ infrastructure for representing and interacting with the gated cytometry data
• d3Network-0.5.2.1 Tools for creating D3 JavaScript network, tree, dendrogram, and<U+000a>Sankey graphs from R
• dHSIC-2.1 Independence Testing via Hilbert Schmidt Independence Criterion
• dada2-1.34.0 Accurate, high-resolution sample inference from amplicon sequencing data
• dagitty-0.3-4 Graphical Analysis of Structural Causal Models
• data.table-1.16.2 Extension of data.frame
• data.tree-1.1.0 General Purpose Hierarchical Data Structure
• datasets built in
• datawizard-0.13.0 Easy Data Wrangling and Statistical Transformations
• date-1.2-42 Functions for Handling Dates
• dbarts-0.9-28 Discrete Bayesian Additive Regression Trees Sampler
• dbplyr-2.5.0 A ‘dplyr’ Back End for Databases
• dbscan-1.2-0 Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms
• dcurver-0.9.2 Utility Functions for Davidian Curves
• ddPCRclust-1.26.0 Clustering algorithm for ddPCR data
• ddalpha-1.3.16 Depth-Based Classification and Calculation of Data Depth
• deSolve-1.40 Solvers for Initial Value Problems of Differential Equations (‘ODE’, ‘DAE’, ‘DDE’)
• deal-1.2-42 Learning Bayesian Networks with Mixed Variables
• debugme-1.2.0 Debug R Packages
• decontam-1.26.0 Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
• decoupleR-2.12.0 decoupleR: Ensemble of computational methods to infer biological activities from omics data
• deldir-2.0-4 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
• dendextend-1.19.0 Extending ‘dendrogram’ Functionality in R
• densEstBayes-1.0-2.2 Density Estimation via Bayesian Inference Engines
• derfinder-1.40.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
• derfinderHelper-1.40.0 derfinder helper package
• desc-1.4.3 Manipulate DESCRIPTION Files
• devtools-2.4.5 Tools to Make Developing R Packages Easier
• dfidx-0.1-0 Indexed Data Frames
• diagram-1.6.5 Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams
• dichromat-2.0-0.1 Color Schemes for Dichromats
• diffcyt-1.26.0 Differential discovery in high-dimensional cytometry via high-resolution clustering
• diffobj-0.3.5 Diffs for R Objects
• digest-0.6.37 Create Compact Hash Digests of R Objects
• dimRed-0.2.6 A Framework for Dimensionality Reduction
• diptest-0.77-1 Hartigan’s Dip Test Statistic for Unimodality - Corrected
• dir.expiry-1.14.0 Managing Expiration for Cache Directories
• directlabels-2024.1.21 Direct Labels for Multicolor Plots
• dismo-1.3-14 Species Distribution Modeling
• distillery-1.2-1 Method Functions for Confidence Intervals and to Distill Information from an Object
• distr-2.9.5 Object Oriented Implementation of Distributions
• distrEx-2.9.5 Extensions of Package ‘distr’
• distributional-0.5.0 Vectorised Probability Distributions
• diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis Package
• dlm-1.1-6.1 Bayesian and Likelihood Analysis of Dynamic Linear Models
• doBy-4.6.24 Groupwise Statistics, LSmeans, Linear Estimates, Utilities
• doMC-1.3.8 Foreach Parallel Adaptor for ‘parallel’
• doParallel-1.0.17 Foreach Parallel Adaptor for the ‘parallel’ Package
• doRNG-1.8.6 Generic Reproducible Parallel Backend for ‘foreach’ Loops
• doSNOW-1.0.20 Foreach Parallel Adaptor for the ‘snow’ Package
• doc2vec-0.2.0 Distributed Representations of Sentences, Documents and Topics
• docopt-0.7.1 Command-Line Interface Specification Language
• docstring-1.0.0 Provides Docstring Capabilities to R Functions
• dotCall64-1.2 Enhanced Foreign Function Interface Supporting Long Vectors
• downlit-0.4.4 Syntax Highlighting and Automatic Linking
• downloader-0.4 Download Files over HTTP and HTTPS
• dplyr-1.1.4 A Grammar of Data Manipulation
• dqrng-0.4.1 Fast Pseudo Random Number Generators
• dr-3.0.10 Methods for Dimension Reduction for Regression
• dreamerr-1.4.0 Error Handling Made Easy
• drgee-1.1.10 Doubly Robust Generalized Estimating Equations
• drugCombo-1.2.1 Drug Interaction Modeling Based on Loewe Additivity Following Harbron’s Approach
• dtangle-2.0.9 Cell Type Deconvolution from Gene Expressions
• dtplyr-1.3.1 Data Table Back-End for ‘dplyr’
• dtw-1.23-1 Dynamic Time Warping Algorithms
• dummies-1.5.6 Create dummy/indicator variables flexibly and efficiently
• dupRadar-1.36.0 Assessment of duplication rates in RNA-Seq datasets
• dygraphs-1.1.1.6 Interface to ‘Dygraphs’ Interactive Time Series Charting Library
• dynamicTreeCut-1.63-1 Methods for Detection of Clusters in Hierarchical Clustering Dendrograms
• e1071-1.7-16 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
• earth-5.3.4 Multivariate Adaptive Regression Splines
• edgeR-4.4.0 Empirical Analysis of Digital Gene Expression Data in R
• egg-0.4.5 Extensions for ‘ggplot2’: Custom Geom, Custom Themes, Plot Alignment, Labelled Panels, Symmetric Scales, and Fixed Panel Size
• ellipse-0.5.0 Functions for Drawing Ellipses and Ellipse-Like Confidence Regions
• ellipsis-0.3.2 Tools for Working with …
• elliptic-1.4-0 Weierstrass and Jacobi Elliptic Functions
• emdbook-1.3.13 Support Functions and Data for “Ecological Models and Data”
• emmeans-1.10.5 Estimated Marginal Means, aka Least-Squares Means
• emoa-0.5-3 Evolutionary Multiobjective Optimization Algorithms
• emulator-1.2-24 Bayesian Emulation of Computer Programs
• energy-1.7-12 E-Statistics: Multivariate Inference via the Energy of Data
• enrichplot-1.26.2 Visualization of Functional Enrichment Result
• ensembldb-2.30.0 Utilities to create and use Ensembl-based annotation databases
• entropy-1.3.1 Estimation of Entropy, Mutual Information and Related Quantities
• epitools-0.5-10.1 Epidemiology Tools
• ergm-4.7.5 Fit, Simulate and Diagnose Exponential-Family Models for Networks
• ergm.count-4.1.2 Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
• ergm.multi-0.2.1.1 Fit, Simulate and Diagnose Exponential-Family Models for Multiple or Multilayer Networks
• escape-2.2.1 Easy single cell analysis platform for enrichment
• estimability-1.5.1 Tools for Assessing Estimability of Linear Predictions
• evaluate-1.0.1 Parsing and Evaluation Tools that Provide More Details than the Default
• evd-2.3-7.1 Functions for Extreme Value Distributions
• expm-1.0-0 Matrix Exponential, Log, ‘etc’
• expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
• extRemes-2.1-4 Extreme Value Analysis
• extraDistr-1.10.0 Additional Univariate and Multivariate Distributions
• extrafont-0.19 Tools for Using Fonts
• extrafontdb-1.0 Package for holding the database for the extrafont package
• fANCOVA-0.6-1 Nonparametric Analysis of Covariance
• factoextra-1.0.7 Extract and Visualize the Results of Multivariate Data Analyses
• fail-1.3 File Abstraction Interface Layer (FAIL)
• fansi-1.0.6 ANSI Control Sequence Aware String Functions
• farver-2.1.2 High Performance Colour Space Manipulation
• fastDummies-1.7.4 Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables
• fastICA-1.2-5.1 FastICA Algorithms to Perform ICA and Projection Pursuit
• fastcluster-1.2.6 Fast Hierarchical Clustering Routines for R and ‘Python’
• fasterize-1.1.0 Fast Polygon to Raster Conversion
• fastlogranktest-0.2.1 A Fast Way to Calculate the p-Value of One or Multiple Log-Rank-Tests
• fastmap-1.2.0 Fast Data Structures
• fastmatch-1.1-4 Fast ‘match()’ Function
• fda-6.2.0 Functional Data Analysis
• fdrtool-1.2.18 Estimation of (Local) False Discovery Rates and Higher Criticism
• fds-1.8 Functional Data Sets
• feather-0.3.5 R Bindings to the Feather ‘API’
• feature-1.2.15 Local Inferential Feature Significance for Multivariate Kernel Density Estimation
• ff-4.5.0 Memory-Efficient Storage of Large Data on Disk and Fast Access Functions
• fftw-1.0-9 Fast FFT and DCT Based on the FFTW Library
• fftwtools-0.9-11 Wrapper for ‘FFTW3’ Includes: One-Dimensional, Two-Dimensional, Three-Dimensional, and Multivariate Transforms
• fgsea-1.32.0 Fast Gene Set Enrichment Analysis
• fields-16.3 Tools for Spatial Data
• filehash-2.4-6 Simple Key-Value Database
• filelock-1.0.3 Portable File Locking
• finalfit-1.0.8 Quickly Create Elegant Regression Results Tables and Plots when Modelling
• findpython-1.0.9 Functions to Find an Acceptable Python Binary
• fishMod-0.29.2 Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta Log-Normal Models
• fitdistrplus-1.2-1 Help to Fit of a Parametric Distribution to Non-Censored or Censored Data
• fixest-0.12.1 Fast Fixed-Effects Estimations
• flashClust-1.01-2 Implementation of optimal hierarchical clustering
• flexclust-1.4-2 Flexible Cluster Algorithms
• flexmix-2.3-19 Flexible Mixture Modeling
• flextable-0.9.7 Functions for Tabular Reporting
• flowAI-1.36.0 Automatic and interactive quality control for flow cytometry data
• flowClean-1.44.0 flowClean
• flowClust-3.44.0 Clustering for Flow Cytometry
• flowCore-2.18.0 flowCore: Basic structures for flow cytometry data
• flowDensity-1.40.0 Sequential Flow Cytometry Data Gating
• flowFP-1.64.0 Fingerprinting for Flow Cytometry
• flowMerge-2.54.0 Cluster Merging for Flow Cytometry Data
• flowPeaks-1.52.0 An R package for flow data clustering
• flowStats-4.18.0 Statistical methods for the analysis of flow cytometry data
• flowViz-1.70.0 Visualization for flow cytometry
• flowWorkspace-4.18.0 Infrastructure for representing and interacting with gated and ungated cytometry data sets.
• fma-2.5 Data Sets from “Forecasting: Methods and Applications” by Makridakis, Wheelwright & Hyndman (1998)
• fmri-1.9.12.1 Analysis of fMRI Experiments
• fontBitstreamVera-0.1.1 Fonts with ‘Bitstream Vera Fonts’ License
• fontLiberation-0.1.0 Liberation Fonts
• fontawesome-0.5.3 Easily Work with ‘Font Awesome’ Icons
• fontquiver-0.2.1 Set of Installed Fonts
• forcats-1.0.0 Tools for Working with Categorical Variables (Factors)
• foreach-1.5.2 Provides Foreach Looping Construct
• forecast-8.23.0 Forecasting Functions for Time Series and Linear Models
• foreign-0.8-87 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, ‘dBase’, …
• formatR-1.14 Format R Code Automatically
• formula.tools-1.7.1 Programmatic Utilities for Manipulating Formulas, Expressions, Calls, Assignments and Other R Objects
• fossil-0.4.0 Palaeoecological and Palaeogeographical Analysis Tools
• fpc-2.2-13 Flexible Procedures for Clustering
• fpp-0.5 Data for “Forecasting: principles and practice”
• fracdiff-1.5-3 Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models
• frbs-3.2-0 Fuzzy Rule-Based Systems for Classification and Regression Tasks
• fresh-0.2.1 Create Custom ‘Bootstrap’ Themes to Use in ‘Shiny’
• fs-1.6.5 Cross-Platform File System Operations Based on ‘libuv’
• furrr-0.3.1 Apply Mapping Functions in Parallel using Futures
• futile.logger-1.4.3 A Logging Utility for R
• futile.options-1.0.1 Futile Options Management
• future-1.34.0 Unified Parallel and Distributed Processing in R for Everyone
• future.apply-1.11.3 Apply Function to Elements in Parallel using Futures
• gWidgets2-1.0-9 Rewrite of gWidgets API for Simplified GUI Construction
• gWidgets2tcltk-1.0-8 Toolkit Implementation of gWidgets2 for tcltk
• gam-1.22-5 Generalized Additive Models
• gamlss-5.4-22 Generalized Additive Models for Location Scale and Shape
• gamlss.data-6.0-6 Data for Generalised Additive Models for Location Scale and Shape
• gamlss.dist-6.1-1 Distributions for Generalized Additive Models for Location Scale and Shape
• gamlss.tr-5.1-9 Generating and Fitting Truncated `gamlss.family’ Distributions
• gamm4-0.2-6 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’
• gap-1.6 Genetic Analysis Package
• gap.datasets-0.0.6 Datasets for ‘gap’
• gapfill-0.9.6-1 Fill Missing Values in Satellite Data
• gargle-1.5.2 Utilities for Working with Google APIs
• gaussquad-1.0-3 Collection of Functions for Gaussian Quadrature
• gbRd-0.4.12 Utilities for Processing Rd Objects and Files
• gbm-2.2.2 Generalized Boosted Regression Models
• gclus-1.3.2 Clustering Graphics
• gcmr-1.0.3 Gaussian Copula Marginal Regression
• gcrma-2.78.0 Background Adjustment Using Sequence Information
• gdalUtils-2.0.3.2 Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities
• gdata-3.0.1 Various R Programming Tools for Data Manipulation
• gdistance-1.6.4 Distances and Routes on Geographical Grids
• gdsfmt-1.42.0 R Interface to CoreArray Genomic Data Structure (GDS) Files
• gdtools-0.4.1 Utilities for Graphical Rendering and Fonts Management
• gee-4.13-27 Generalized Estimation Equation Solver
• geeM-0.10.1 Solve Generalized Estimating Equations
• geepack-1.3.12 Generalized Estimating Equation Package
• geex-1.1.1 An API for M-Estimation
• geiger-2.0.11 Analysis of Evolutionary Diversification
• geneLenDataBase 1.42.0 Package Not Found
• genefilter-1.88.0 genefilter: methods for filtering genes from high-throughput experiments
• geneplotter-1.84.0 Graphics related functions for Bioconductor
• generics-0.1.3 Common S3 Generics not Provided by Base R Methods Related to Model Fitting
• genoPlotR-0.8.11 Plot Publication-Grade Gene and Genome Maps
• genomation-1.38.0 Summary, annotation and visualization of genomic data
• geojsonsf-2.0.3 GeoJSON to Simple Feature Converter
• geometries-0.2.4 Convert Between R Objects and Geometric Structures
• geometry-0.5.0 Mesh Generation and Surface Tessellation
• gert-2.1.4 Simple Git Client for R
• getopt-1.20.4 C-Like ‘getopt’ Behavior
• gfonts-0.2.0 Offline ‘Google’ Fonts for ‘Markdown’ and ‘Shiny’
• ggExtra-0.10.1 Add Marginal Histograms to ‘ggplot2’, and More ‘ggplot2’ Enhancements
• ggbeeswarm-0.7.2 Categorical Scatter (Violin Point) Plots
• ggbio-1.54.0 Visualization tools for genomic data
• ggcyto-1.34.0 Visualize Cytometry data with ggplot
• ggdag-0.2.13 Analyze and Create Elegant Directed Acyclic Graphs
• ggdendro-0.2.0 Create Dendrograms and Tree Diagrams Using ‘ggplot2’
• ggdist-3.3.2 Visualizations of Distributions and Uncertainty
• ggfan-0.1.3 Summarise a Distribution Through Coloured Intervals
• ggforce-0.4.2 Accelerating ‘ggplot2’
• ggformula-0.12.0 Formula Interface to the Grammar of Graphics
• ggfun-0.1.7 Miscellaneous Functions for ‘ggplot2’
• ggh4x-0.2.8 Hacks for ‘ggplot2’
• ggnetwork-0.5.13 Geometries to Plot Networks with ‘ggplot2’
• ggnewscale-0.5.0 Multiple Fill and Colour Scales in ‘ggplot2’
• ggplot2-3.5.1 Create Elegant Data Visualisations Using the Grammar of Graphics
• ggplotify-0.1.2 Convert Plot to ‘grob’ or ‘ggplot’ Object
• ggpointdensity-0.1.0 A Cross Between a 2D Density Plot and a Scatter Plot
• ggpubr-0.6.0 ‘ggplot2’ Based Publication Ready Plots
• ggraph-2.2.1 An Implementation of Grammar of Graphics for Graphs and Networks
• ggrastr-1.0.2 Rasterize Layers for ‘ggplot2’
• ggrepel-0.9.6 Automatically Position Non-Overlapping Text Labels with ‘ggplot2’
• ggridges-0.5.6 Ridgeline Plots in ‘ggplot2’
• ggsci-3.2.0 Scientific Journal and Sci-Fi Themed Color Palettes for ‘ggplot2’
• ggseqlogo-0.2 A ‘ggplot2’ Extension for Drawing Publication-Ready Sequence Logos
• ggsignif-0.6.4 Significance Brackets for ‘ggplot2’
• ggstance-0.3.7 Horizontal ‘ggplot2’ Components
• ggstats-0.7.0 Extension to ‘ggplot2’ for Plotting Stats
• ggtangle-0.0.4 Draw Network with Data
• ggthemes-5.1.0 Extra Themes, Scales and Geoms for ‘ggplot2’
• ggtree-3.14.0 an R package for visualization of tree and annotation data
• ggvenn-0.1.10 Draw Venn Diagram by ‘ggplot2’
• ggvis-0.4.9 Interactive Grammar of Graphics
• gh-1.4.1 ‘GitHub’ ‘API’
• git2r-0.35.0 Provides Access to Git Repositories
• gitcreds-0.1.2 Query ‘git’ Credentials from ‘R’
• glasso-1.11 Graphical Lasso: Estimation of Gaussian Graphical Models
• gld-2.6.6 Estimation and Use of the Generalised (Tukey) Lambda Distribution
• gllvm-1.4.3 Generalized Linear Latent Variable Models
• glmmML-1.1.7 Generalized Linear Models with Clustering
• glmmTMB-1.1.10 Generalized Linear Mixed Models using Template Model Builder
• glmnet-4.1-8 Lasso and Elastic-Net Regularized Generalized Linear Models
• globals-0.16.3 Identify Global Objects in R Expressions
• globaltest-5.60.0 Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
• glue-1.8.0 Interpreted String Literals
• gmm-1.8 Generalized Method of Moments and Generalized Empirical Likelihood
• gmodels-2.19.1 Various R Programming Tools for Model Fitting
• gmp-0.7-5 Multiple Precision Arithmetic
• gnumeric-0.7-10 Read Data from Files Readable by ‘gnumeric’
• goftest-1.2-3 Classical Goodness-of-Fit Tests for Univariate Distributions
• goldilocks-0.3.0 Goldilocks Adaptive Trial Designs for Time-to-Event Endpoints
• gomms-1.0 GLM-Based Ordination Method
• googledrive-2.1.1 An Interface to Google Drive
• googlesheets4-1.1.1 Access Google Sheets using the Sheets API V4
• goseq-1.58.0 Gene Ontology analyser for RNA-seq and other length biased data
• gower-1.0.1 Gower’s Distance
• gplots-3.2.0 Various R Programming Tools for Plotting Data
• grDevices built in
• grImport2-0.3-3 Importing ‘SVG’ Graphics
• graph-1.84.0 graph: A package to handle graph data structures
• graphics built in
• graphite-1.52.0 GRAPH Interaction from pathway Topological Environment
• graphlayouts-1.2.1 Additional Layout Algorithms for Network Visualizations
• grf-2.4.0 Generalized Random Forests
• grid built in
• gridBase-0.4-7 Integration of base and grid graphics
• gridExtra-2.3 Miscellaneous Functions for “Grid” Graphics
• gridGraphics-0.5-1 Redraw Base Graphics Using ‘grid’ Graphics
• grpreg-3.5.0 Regularization Paths for Regression Models with Grouped Covariates
• gsDesign-3.6.5 Group Sequential Design
• gsalib-2.2.1 Utility Functions for ‘GATK’
• gsignal-0.3-7 Signal Processing
• gsl-2.1-8 Wrapper for the Gnu Scientific Library
• gsmoothr-0.1.7 Smoothing tools
• gson-0.1.0 Base Class and Methods for ‘gson’ Format
• gsw-1.2-0 Gibbs Sea Water Functions
• gt-0.11.1 Easily Create Presentation-Ready Display Tables
• gtable-0.3.6 Arrange ‘Grobs’ in Tables
• gtools-3.9.5 Various R Programming Tools
• gtsummary-2.0.3 Presentation-Ready Data Summary and Analytic Result Tables
• h2o-3.44.0.3 R Interface for the ‘H2O’ Scalable Machine Learning Platform
• hahmmr-1.0.0 Haplotype-Aware Hidden Markov Model for RNA
• hal9001-0.4.6 The Scalable Highly Adaptive Lasso
• haldensify-0.2.3 Highly Adaptive Lasso Conditional Density Estimation
• hardhat-1.4.0 Construct Modeling Packages
• harmony-1.2.1 Fast, Sensitive, and Accurate Integration of Single Cell Data
• hash-2.2.6.3 Full Featured Implementation of Hash Tables/Associative Arrays/Dictionaries
• haven-2.5.4 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files
• hdf5r-1.3.11 Interface to the ‘HDF5’ Binary Data Format
• hdm-0.3.2 High-Dimensional Metrics
• hdrcde-3.4 Highest Density Regions and Conditional Density Estimation
• heatmap3-1.1.9 An Improved Heatmap Package
• heatmaply-1.5.0 Interactive Cluster Heat Maps Using ‘plotly’ and ‘ggplot2’
• here-1.0.1 A Simpler Way to Find Your Files
• hexbin-1.28.5 Hexagonal Binning Routines
• hgu133plus2.db 3.13.0 Package Not Found
• highr-0.11 Syntax Highlighting for R Source Code
• hms-1.1.3 Pretty Time of Day
• htmlTable-2.4.3 Advanced Tables for Markdown/HTML
• htmltools-0.5.8.1 Tools for HTML
• htmlwidgets-1.6.4 HTML Widgets for R
• httpcode-0.3.0 ‘HTTP’ Status Code Helper
• httpuv-1.6.15 HTTP and WebSocket Server Library
• httr-1.4.7 Tools for Working with URLs and HTTP
• httr2-1.0.6 Perform HTTP Requests and Process the Responses
• huge-1.3.5 High-Dimensional Undirected Graph Estimation
• hunspell-3.0.5 High-Performance Stemmer, Tokenizer, and Spell Checker
• hwriter-1.3.2.1 HTML Writer - Outputs R Objects in HTML Format
• hypergeo-1.2-13 The Gauss Hypergeometric Function
• ica-1.0-3 Independent Component Analysis
• idr-1.3 Irreproducible Discovery Rate
• ids-1.0.1 Generate Random Identifiers
• ie2misc-0.9.1 Irucka Embry’s Miscellaneous USGS Functions
• igraph-2.1.1 Network Analysis and Visualization
• illuminaio-0.48.0 Parsing Illumina Microarray Output Files
• image.binarization-0.1.3 Binarize Images for Enhancing Optical Character Recognition
• imager-1.0.2 Image Processing Library Based on ‘CImg’
• imagerExtra-1.3.2 Extra Image Processing Library Based on ‘imager’
• impute-1.80.0 impute: Imputation for microarray data
• ineq-0.2-13 Measuring Inequality, Concentration, and Poverty
• influenceR-0.1.5 Software Tools to Quantify Structural Importance of Nodes in a Network
• infotheo-1.2.0.1 Information-Theoretic Measures
• ini-0.3.1 Read and Write ‘.ini’ Files
• inline-0.3.20 Functions to Inline C, C++, Fortran Function Calls from R
• insight-0.20.5 Easy Access to Model Information for Various Model Objects
• interactiveDisplayBase-1.44.0 Base package for enabling powerful shiny web displays of Bioconductor objects
• intergraph-2.0-4 Coercion Routines for Network Data Objects
• interp-1.1-6 Interpolation Methods
• interpretR-0.2.5 Binary Classifier and Regression Model Interpretation Functions
• intervals-0.15.5 Tools for Working with Points and Intervals
• intrinsicDimension-1.2.0 Intrinsic Dimension Estimation
• inum-1.0-5 Interval and Enum-Type Representation of Vectors
• ipred-0.9-15 Improved Predictors
• irace-3.5 Iterated Racing for Automatic Algorithm Configuration
• irlba-2.3.5.1 Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices
• ismev-1.42 An Introduction to Statistical Modeling of Extreme Values
• isoband-0.2.7 Generate Isolines and Isobands from Regularly Spaced Elevation Grids
• isva-1.9 Independent Surrogate Variable Analysis
• iterators-1.0.14 Provides Iterator Construct
• itertools-0.1-3 Iterator Tools
• janeaustenr-1.0.0 Jane Austen’s Complete Novels
• jiebaR-0.11 Chinese Text Segmentation
• jiebaRD-0.1 Chinese Text Segmentation Data for jiebaR Package
• jomo-2.7-6 Multilevel Joint Modelling Multiple Imputation
• jpeg-0.1-10 Read and write JPEG images
• jquerylib-0.1.4 Obtain ‘jQuery’ as an HTML Dependency Object
• jsonify-1.2.2 Convert Between ‘R’ Objects and Javascript Object Notation (JSON)
• jsonlite-1.8.9 A Simple and Robust JSON Parser and Generator for R
• jstable-1.3.6 Create Tables from Different Types of Regression
• juicyjuice-0.1.0 Inline CSS Properties into HTML Tags Using ‘juice’
• kableExtra-1.4.0 Construct Complex Table with ‘kable’ and Pipe Syntax
• kde1d-1.0.7 Univariate Kernel Density Estimation
• kedd-1.0.4 Kernel Estimator and Bandwidth Selection for Density and Its Derivatives
• kernlab-0.9-33 Kernel-Based Machine Learning Lab
• kinship2-1.9.6.1 Pedigree Functions
• klaR-1.7-3 Classification and Visualization
• knitr-1.49 A General-Purpose Package for Dynamic Report Generation in R
• kohonen-3.0.12 Supervised and Unsupervised Self-Organising Maps
• ks-1.14.3 Kernel Smoothing
• labdsv-2.1-0 Ordination and Multivariate Analysis for Ecology
• labeling-0.4.3 Axis Labeling
• labelled-2.13.0 Manipulating Labelled Data
• laeken-0.5.3 Estimation of Indicators on Social Exclusion and Poverty
• lambda.r-1.2.4 Modeling Data with Functional Programming
• lars-1.3 Least Angle Regression, Lasso and Forward Stagewise
• lassosum 0.4.5 Package Not Found
• later-1.3.2 Utilities for Scheduling Functions to Execute Later with Event Loops
• lattice-0.22-6 Trellis Graphics for R
• latticeExtra-0.6-30 Extra Graphical Utilities Based on Lattice
• lava-1.8.0 Latent Variable Models
• lavaan-0.6-19 Latent Variable Analysis
• lazy-1.2-18 Lazy Learning for Local Regression
• lazyeval-0.2.2 Lazy (Non-Standard) Evaluation
• lda-1.5.2 Collapsed Gibbs Sampling Methods for Topic Models
• ldbounds-2.0.2 Lan-DeMets Method for Group Sequential Boundaries
• leafem-0.2.3 ‘leaflet’ Extensions for ‘mapview’
• leaflet-2.2.2 Create Interactive Web Maps with the JavaScript ‘Leaflet’ Library
• leaflet.providers-2.0.0 Leaflet Providers
• leafsync-0.1.0 Small Multiples for Leaflet Web Maps
• leaps-3.2 Regression Subset Selection
• leiden-0.4.3.1 R Implementation of Leiden Clustering Algorithm
• lhs-1.2.0 Latin Hypercube Samples
• libcoin-1.0-10 Linear Test Statistics for Permutation Inference
• lifecycle-1.0.4 Manage the Life Cycle of your Package Functions
• limSolve-1.5.7.1 Solving Linear Inverse Models
• limma-3.62.1 Linear Models for Microarray and Omics Data
• linkcomm-1.0-14 Tools for Generating, Visualizing, and Analysing Link Communities in Networks
• linprog-0.9-4 Linear Programming / Optimization
• liquidSVM-1.2.4 A Fast and Versatile SVM Package
• listenv-0.9.1 Environments Behaving (Almost) as Lists
• lme4-1.1-35.5 Linear Mixed-Effects Models using ‘Eigen’ and S4
• lmerTest-3.1-3 Tests in Linear Mixed Effects Models
• lmom-3.2 L-Moments
• lmtest-0.9-40 Testing Linear Regression Models
• lobstr-1.1.2 Visualize R Data Structures with Trees
• locfdr-1.1-8 Computes Local False Discovery Rates
• locfit-1.5-9.10 Local Regression, Likelihood and Density Estimation
• log4r-0.4.4 A Fast and Lightweight Logging System for R, Based on ‘log4j’
• logcondens-2.1.8 Estimate a Log-Concave Probability Density from Iid Observations
• logger-0.4.0 A Lightweight, Modern and Flexible Logging Utility
• logistf-1.26.0 Firth’s Bias-Reduced Logistic Regression
• logspline-2.1.22 Routines for Logspline Density Estimation
• longitudinal-1.1.13 Analysis of Multiple Time Course Data
• longmemo-1.1-3 Statistics for Long-Memory Processes (Book Jan Beran), and Related Functionality
• loo-2.8.0 Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
• lpSolve-5.6.22 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programs
• lpSolveAPI-5.5.2.0-17.12 R Interface to ‘lp_solve’ Version 5.5.2.0
• lpsymphony-1.34.0 Symphony integer linear programming solver in R
• lqa-1.0-3 Penalized Likelihood Inference for GLMs
• lsa-0.73.3 Latent Semantic Analysis
• lsei-1.3-0 Solving Least Squares or Quadratic Programming Problems under Equality/Inequality Constraints
• lslx-0.6.11 Semi-Confirmatory Structural Equation Modeling via Penalized Likelihood or Least Squares
• lubridate-1.9.3 Make Dealing with Dates a Little Easier
• lumi-2.58.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
• lwgeom-0.2-14 Bindings to Selected ‘liblwgeom’ Functions for Simple Features
• mRMRe-2.1.2.2 Parallelized Minimum Redundancy, Maximum Relevance (mRMR)
• maSigPro-1.78.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
• magic-1.6-1 Create and Investigate Magic Squares
• magick-2.8.5 Advanced Graphics and Image-Processing in R
• magrittr-2.0.3 A Forward-Pipe Operator for R
• manipulateWidget-0.11.1 Add Even More Interactivity to Interactive Charts
• mapproj-1.2.11 Map Projections
• maps-3.4.2.1 Draw Geographical Maps
• maptools-1.1-8 Tools for Handling Spatial Objects
• markdown-1.13 Render Markdown with ‘commonmark’
• marray-1.84.0 Exploratory analysis for two-color spotted microarray data
• mathjaxr-1.6-0 Using ‘Mathjax’ in Rd Files
• matlab-1.0.4.1 ‘MATLAB’ Emulation Package
• matrixStats-1.4.1 Functions that Apply to Rows and Columns of Matrices (and to Vectors)
• matrixcalc-1.0-6 Collection of Functions for Matrix Calculations
• maxLik-1.5-2.1 Maximum Likelihood Estimation and Related Tools
• maxlike-0.1-11 Model Species Distributions by Estimating the Probability of Occurrence Using Presence-Only Data
• maxnet-0.1.4 Fitting ‘Maxent’ Species Distribution Models with ‘glmnet’
• mboost-2.9-11 Model-Based Boosting
• mclogit-0.9.6 Multinomial Logit Models, with or without Random Effects or Overdispersion
• mclust-6.1.1 Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
• mcmc-0.9-8 Markov Chain Monte Carlo
• mcmcse-1.5-0 Monte Carlo Standard Errors for MCMC
• mda-0.5-5 Mixture and Flexible Discriminant Analysis
• medflex-0.6-10 Flexible Mediation Analysis Using Natural Effect Models
• mediation-4.5.0 Causal Mediation Analysis
• memisc-0.99.31.8.1 Management of Survey Data and Presentation of Analysis Results
• memoise-2.0.1 ‘Memoisation’ of Functions
• memuse-4.2-3 Memory Estimation Utilities
• metaMA-3.1.3 Meta-Analysis for MicroArrays
• metadat-1.2-0 Meta-Analysis Datasets
• metafor-4.6-0 Meta-Analysis Package for R
• metap-1.11 Meta-Analysis of Significance Values
• metapod-1.14.0 Meta-Analyses on P-Values of Differential Analyses
• methods built in
• methylumi-2.52.0 Handle Illumina methylation data
• mets-1.3.4 Analysis of Multivariate Event Times
• mgcv-1.9-1 Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
• mgsub-1.7.3 Safe, Multiple, Simultaneous String Substitution
• mhsmm-0.4.21 Inference for Hidden Markov and Semi-Markov Models
• mi-1.1 Missing Data Imputation and Model Checking
• mia-1.14.0 Microbiome analysis
• mice-3.16.0 Multivariate Imputation by Chained Equations
• miceadds-3.17-44 Some Additional Multiple Imputation Functions, Especially for ‘mice’
• microbenchmark-1.5.0 Accurate Timing Functions
• mime-0.12 Map Filenames to MIME Types
• minerva-1.5.10 Maximal Information-Based Nonparametric Exploration for Variable Analysis
• minfi-1.52.1 Analyze Illumina Infinium DNA methylation arrays
• miniUI-0.1.1.1 Shiny UI Widgets for Small Screens
• minpack.lm-1.2-4 R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK, Plus Support for Bounds
• minqa-1.2.8 Derivative-Free Optimization Algorithms by Quadratic Approximation
• minty-0.0.4 Minimal Type Guesser
• mirt-1.43 Multidimensional Item Response Theory
• misc3d-0.9-1 Miscellaneous 3D Plots
• miscTools-0.6-28 Miscellaneous Tools and Utilities
• missForest-1.5 Nonparametric Missing Value Imputation using Random Forest
• missMDA-1.19 Handling Missing Values with Multivariate Data Analysis
• missMethyl-1.40.0 Analysing Illumina HumanMethylation BeadChip Data
• mitml-0.4-5 Tools for Multiple Imputation in Multilevel Modeling
• mitools-2.4 Tools for Multiple Imputation of Missing Data
• mixOmics-6.30.0 Omics Data Integration Project
• mixsqp-0.3-54 Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions
• mixtools-2.0.0 Tools for Analyzing Finite Mixture Models
• mlbench-2.1-5 Machine Learning Benchmark Problems
• mlegp-3.1.9 Maximum Likelihood Estimates of Gaussian Processes
• mlogit-1.1-1 Multinomial Logit Models
• mlr-2.19.2 Machine Learning in R
• mlrMBO-1.1.5.1 Bayesian Optimization and Model-Based Optimization of Expensive Black-Box Functions
• mltools-0.3.5 Machine Learning Tools
• mnormt-2.1.1 The Multivariate Normal and t Distributions, and Their Truncated Versions
• modelr-0.1.11 Modelling Functions that Work with the Pipe
• modeltools-0.2-23 Tools and Classes for Statistical Models
• momentfit-0.5 Methods of Moments
• moments-0.14.1 Moments, Cumulants, Skewness, Kurtosis and Related Tests
• mosaicCore-0.9.4.0 Common Utilities for Other MOSAIC-Family Packages
• motifStack-1.50.0 Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
• motifmatchr-1.28.0 Fast Motif Matching in R
• mpath-0.4-2.26 Regularized Linear Models
• msigdbr-7.5.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
• msm-1.8.2 Multi-State Markov and Hidden Markov Models in Continuous Time
• mstate-0.3.3 Data Preparation, Estimation and Prediction in Multi-State Models
• multcomp-1.4-26 Simultaneous Inference in General Parametric Models
• multcompView-0.1-10 Visualizations of Paired Comparisons
• multicool-1.0.1 Permutations of Multisets in Cool-Lex Order
• multipol-1.0-9 Multivariate Polynomials
• multitaper-1.0-17 Spectral Analysis Tools using the Multitaper Method
• multtest-2.62.0 Resampling-based multiple hypothesis testing
• munsell-0.5.1 Utilities for Using Munsell Colours
• muscat-1.20.0 Multi-sample multi-group scRNA-seq data analysis tools
• mutoss-0.1-13 Unified Multiple Testing Procedures
• mvabund-4.2.1 Statistical Methods for Analysing Multivariate Abundance Data
• mvnfast-0.2.8 Fast Multivariate Normal and Student’s t Methods
• mvtnorm-1.3-2 Multivariate Normal and t Distributions
• mzID-1.44.0 An mzIdentML parser for R
• mzR-2.40.0 parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
• nabor-0.5.0 Wraps ‘libnabo’, a Fast K Nearest Neighbour Library for Low Dimensions
• naniar-1.1.0 Data Structures, Summaries, and Visualisations for Missing Data
• natserv-1.0.0 ‘NatureServe’ Interface
• naturalsort-0.1.3 Natural Ordering
• ncbit-2013.03.29.1 Retrieve and Build NBCI Taxonomic Data
• ncdf4-1.23 Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files
• ncdfFlow-2.52.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
• network-1.18.2 Classes for Relational Data
• networkDynamic-0.11.5 Dynamic Extensions for Network Objects
• networkLite-1.0.5 An Simplified Implementation of the ‘network’ Package Functionality
• neuRosim-0.2-14 Simulate fMRI Data
• neuralnet-1.44.2 Training of Neural Networks
• ngspatial-1.2-2 Fitting the Centered Autologistic and Sparse Spatial Generalized Linear Mixed Models for Areal Data
• nleqslv-3.3.5 Solve Systems of Nonlinear Equations
• nlme-3.1-166 Linear and Nonlinear Mixed Effects Models
• nloptr-2.1.1 R Interface to NLopt
• nlsem-0.8-1 Fitting Structural Equation Mixture Models
• nnet-7.3-19 Feed-Forward Neural Networks and Multinomial Log-Linear Models
• nnls-1.6 The Lawson-Hanson Algorithm for Non-Negative Least Squares (NNLS)
• nonnest2-0.5-8 Tests of Non-Nested Models
• nor1mix-1.3-3 Normal aka Gaussian 1-d Mixture Models
• norm-1.0-11.1 Analysis of Multivariate Normal Datasets with Missing Values
• nortest-1.0-4 Tests for Normality
• np-0.60-17 Nonparametric Kernel Smoothing Methods for Mixed Data Types
• npsurv-0.5-0 Nonparametric Survival Analysis
• numDeriv-2016.8-1.1 Accurate Numerical Derivatives
• numbat-1.4.2 Haplotype-Aware CNV Analysis from scRNA-Seq
• oai-0.4.0 General Purpose ‘Oai-PMH’ Services Client
• oce-1.8-3 Analysis of Oceanographic Data
• oddsratio-2.0.1 Odds Ratio Calculation for GAM(M)s & GLM(M)s
• officer-0.6.7 Manipulation of Microsoft Word and PowerPoint Documents
• oligo-1.70.0 Preprocessing tools for oligonucleotide arrays
• oligoClasses-1.68.0 Classes for high-throughput arrays supported by oligo and crlmm
• ontologyIndex-2.12 Reading Ontologies into R
• oompaBase-3.2.9 Class Unions, Matrix Operations, and Color Schemes for OOMPA
• oompaData-3.1.4 Data to Illustrate OOMPA Algorithms
• openCyto-2.18.0 Hierarchical Gating Pipeline for flow cytometry data
• openair-2.18-2 Tools for the Analysis of Air Pollution Data
• openssl-2.2.2 Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
• openxlsx-4.2.7.1 Read, Write and Edit xlsx Files
• operator.tools-1.6.3 Utilities for Working with R’s Operators
• optextras-2019-12.4 Tools to Support Optimization Possibly with Bounds and Masks
• optimParallel-1.0-2 Parallel Version of the L-BFGS-B Optimization Method
• optimr-2019-12.16 A Replacement and Extension of the ‘optim’ Function
• optimx-2023-10.21 Expanded Replacement and Extension of the ‘optim’ Function
• optmatch-0.10.8 Functions for Optimal Matching
• optparse-1.7.5 Command Line Option Parser
• ordinal-2023.12-4.1 Regression Models for Ordinal Data
• org.Hs.eg.db 3.20.0 Package Not Found
• org.Mm.eg.db 3.20.0 Package Not Found
• org.Rn.eg.db 3.20.0 Package Not Found
• origami-1.0.7 Generalized Framework for Cross-Validation
• oro.nifti-0.11.4 Rigorous - ‘NIfTI’ + ‘ANALYZE’ + ‘AFNI’ : Input / Output
• orthopolynom-1.0-6.1 Collection of Functions for Orthogonal and Orthonormal Polynomials
• osqp-0.6.3.3 Quadratic Programming Solver using the ‘OSQP’ Library
• outliers-0.15 Tests for Outliers
• pROC-1.18.5 Display and Analyze ROC Curves
• pRoloc-1.46.0 A unifying bioinformatics framework for spatial proteomics
• pRolocGUI-2.16.0 Interactive visualisation of spatial proteomics data
• pRolocdata 1.44.0 Package Not Found
• packrat-0.9.2 A Dependency Management System for Projects and their R Package Dependencies
• pacman-0.5.1 Package Management Tool
• pammtools-0.5.93 Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis
• pamr-1.57 Pam: Prediction Analysis for Microarrays
• pan-1.9 Multiple Imputation for Multivariate Panel or Clustered Data
• parallel built in
• parallelDist-0.2.6 Parallel Distance Matrix Computation using Multiple Threads
• parallelMap-1.5.1 Unified Interface to Parallelization Back-Ends
• parallelly-1.39.0 Enhancing the ‘parallel’ Package
• parsedate-1.3.1 Recognize and Parse Dates in Various Formats, Including All ISO 8601 Formats
• party-1.3-17 A Laboratory for Recursive Partytioning
• partykit-1.2-22 A Toolkit for Recursive Partytioning
• pastecs-1.4.2 Package for Analysis of Space-Time Ecological Series
• patchwork-1.3.0 The Composer of Plots
• pathview-1.46.0 a tool set for pathway based data integration and visualization
• pbapply-1.7-2 Adding Progress Bar to ‘*apply’ Functions
• pbivnorm-0.6.0 Vectorized Bivariate Normal CDF
• pbkrtest-0.5.3 Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models
• pbmcapply-1.5.1 Tracking the Progress of Mc*pply with Progress Bar
• pcaMethods-1.98.0 A collection of PCA methods
• pcaPP-2.0-5 Robust PCA by Projection Pursuit
• pdp-0.8.2 Partial Dependence Plots
• pec-2023.04.12 Prediction Error Curves for Risk Prediction Models in Survival Analysis
• penalized-0.9-52 L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model
• penfa-0.1.1 Single- And Multiple-Group Penalized Factor Analysis
• peperr-1.5 Parallelised Estimation of Prediction Error
• performance-0.12.4 Assessment of Regression Models Performance
• perm-1.0-0.4 Exact or Asymptotic Permutation Tests
• permute-0.9-7 Functions for Generating Restricted Permutations of Data
• phangorn-2.12.1 Phylogenetic Reconstruction and Analysis
• pheatmap-1.0.12 Pretty Heatmaps
• phylobase-0.8.12 Base Package for Phylogenetic Structures and Comparative Data
• phyloseq-1.50.0 Handling and analysis of high-throughput microbiome census data
• phytools-2.3-0 Phylogenetic Tools for Comparative Biology (and Other Things)
• pillar-1.9.0 Coloured Formatting for Columns
• pim-2.0.2 Fit Probabilistic Index Models
• pinfsc50-1.3.0 Sequence (‘FASTA’), Annotation (‘GFF’) and Variants (‘VCF’) for 17 Samples of ‘P. Infestans” and 1 ‘P. Mirabilis’
• pixmap-0.4-13 Bitmap Images / Pixel Maps
• pkgbuild-1.4.5 Find Tools Needed to Build R Packages
• pkgconfig-2.0.3 Private Configuration for ‘R’ Packages
• pkgdown-2.1.1 Make Static HTML Documentation for a Package
• pkgload-1.4.0 Simulate Package Installation and Attach
• pkgmaker-0.32.10 Development Utilities for R Packages
• plogr-0.2.0 The ‘plog’ C++ Logging Library
• plot3D-1.4.1 Plotting Multi-Dimensional Data
• plot3Drgl-1.0.4 Plotting Multi-Dimensional Data - Using ‘rgl’
• plotly-4.10.4 Create Interactive Web Graphics via ‘plotly.js’
• plotmo-3.6.4 Plot a Model’s Residuals, Response, and Partial Dependence Plots
• plotrix-3.8-4 Various Plotting Functions
• pls-2.8-5 Partial Least Squares and Principal Component Regression
• plyr-1.8.9 Tools for Splitting, Applying and Combining Data
• plyranges-1.26.0 A fluent interface for manipulating GenomicRanges
• pmp-1.18.0 Peak Matrix Processing and signal batch correction for metabolomics datasets
• png-0.1-8 Read and write PNG images
• poLCA-1.6.0.1 Polytomous Variable Latent Class Analysis
• polspline-1.1.25 Polynomial Spline Routines
• polyclip-1.10-7 Polygon Clipping
• polycor-0.8-1 Polychoric and Polyserial Correlations
• polynom-1.4-1 A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations
• posterior-1.6.0 Tools for Working with Posterior Distributions
• poweRlaw-0.80.0 Analysis of Heavy Tailed Distributions
• ppcor-1.1 Partial and Semi-Partial (Part) Correlation
• prabclus-2.3-4 Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data
• pracma-2.4.4 Practical Numerical Math Functions
• praise-1.0.0 Praise Users
• preprocessCore-1.68.0 A collection of pre-processing functions
• preseqR-4.0.0 Predicting Species Accumulation Curves
• prettyGraphs-2.1.6 Publication-Quality Graphics
• prettyunits-1.2.0 Pretty, Human Readable Formatting of Quantities
• princurve-2.1.6 Fit a Principal Curve in Arbitrary Dimension
• processx-3.8.4 Execute and Control System Processes
• prodlim-2024.06.25 Product-Limit Estimation for Censored Event History Analysis
• profileModel-0.6.1 Profiling Inference Functions for Various Model Classes
• proftools-0.99-3 Profile Output Processing Tools for R
• profvis-0.4.0 Interactive Visualizations for Profiling R Code
• progress-1.2.3 Terminal Progress Bars
• progressr-0.15.1 An Inclusive, Unifying API for Progress Updates
• projpred-2.8.0 Projection Predictive Feature Selection
• promises-1.3.0 Abstractions for Promise-Based Asynchronous Programming
• proto-1.0.0 Prototype Object-Based Programming
• proxy-0.4-27 Distance and Similarity Measures
• proxyC-0.4.1 Computes Proximity in Large Sparse Matrices
• pryr-0.1.6 Tools for Computing on the Language
• ps-1.8.1 List, Query, Manipulate System Processes
• pscl-1.5.9 Political Science Computational Laboratory
• pspline-1.0-20 Penalized Smoothing Splines
• psych-2.4.6.26 Procedures for Psychological, Psychometric, and Personality Research
• pulsar-0.3.11 Parallel Utilities for Lambda Selection along a Regularization Path
• purrr-1.0.2 Functional Programming Tools
• pvclust-2.2-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
• pwalign-1.2.0 Perform pairwise sequence alignments
• qap-0.1-2 Heuristics for the Quadratic Assignment Problem (QAP)
• qgam-1.3.4 Smooth Additive Quantile Regression Models
• qgraph-1.9.8 Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
• qlcMatrix-0.9.8 Utility Sparse Matrix Functions for Quantitative Language Comparison
• qqconf-1.3.2 Creates Simultaneous Testing Bands for QQ-Plots
• qqman-0.1.9 Q-Q and Manhattan Plots for GWAS Data
• qrng-0.0-10 (Randomized) Quasi-Random Number Generators
• qrnn-2.1.1 Quantile Regression Neural Network
• quadprog-1.5-8 Functions to Solve Quadratic Programming Problems
• quanteda-4.1.0 Quantitative Analysis of Textual Data
• quantmod-0.4.26 Quantitative Financial Modelling Framework
• quantreg-5.99.1 Quantile Regression
• quantsmooth-1.72.0 Quantile smoothing and genomic visualization of array data
• questionr-0.7.8 Functions to Make Surveys Processing Easier
• qvalue-2.38.0 Q-value estimation for false discovery rate control
• r2rtf-1.1.1 Easily Create Production-Ready Rich Text Format (RTF) Tables and Figures
• rARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD Problems
• rGADEM-2.54.0 de novo motif discovery
• rJava-1.0-11 Low-Level R to Java Interface
• ragg-1.3.3 Graphic Devices Based on AGG
• rainbow-3.8 Bagplots, Boxplots and Rainbow Plots for Functional Data
• random-0.2.6 True Random Numbers using RANDOM.ORG
• randomForest-4.7-1.2 Breiman and Cutlers Random Forests for Classification and Regression
• randomForestSRC-3.3.1 Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
• randomcoloR-1.1.0.1 Generate Attractive Random Colors
• randtoolbox-2.0.5 Toolbox for Pseudo and Quasi Random Number Generation and Random Generator Tests
• rangeModelMetadata-0.1.5 Provides Templates for Metadata Files Associated with Species Range Models
• ranger-0.17.0 A Fast Implementation of Random Forests
• rapidjsonr-1.2.0 ‘Rapidjson’ C++ Header Files
• rappdirs-0.3.3 Application Directories: Determine Where to Save Data, Caches, and Logs
• raster-3.6-30 Geographic Data Analysis and Modeling
• rasterVis-0.51.6 Visualization Methods for Raster Data
• ratelimitr-0.4.1 Rate Limiting for R
• rbibutils-2.3 Read ‘Bibtex’ Files and Convert Between Bibliography Formats
• rbiom-1.0.3 Read/Write, Analyze, and Visualize ‘BIOM’ Data
• rbison-1.0.0 Interface to the ‘USGS’ ‘BISON’ API
• rcmdcheck-1.4.0 Run ‘R CMD check’ from ‘R’ and Capture Results
• rda-1.2-1 Shrunken Centroids Regularized Discriminant Analysis
• rdrop2-0.8.2.1 Programmatic Interface to the ‘Dropbox’ API
• reactR-0.6.1 React Helpers
• reactable-0.4.4 Interactive Data Tables for R
• reactome.db 1.89.0 Package Not Found
• readODS-2.3.1 Read and Write ODS Files
• readbitmap-0.1.5 Simple Unified Interface to Read Bitmap Images (BMP,JPEG,PNG,TIFF)
• reader-1.0.6 Suite of Functions to Flexibly Read Data from Files
• readr-2.1.5 Read Rectangular Text Data
• readxl-1.4.3 Read Excel Files
• rebird-1.3.0 R Client for the eBird Database of Bird Observations
• recipes-1.1.0 Preprocessing and Feature Engineering Steps for Modeling
• reformulas-0.4.0 Machinery for Processing Random Effect Formulas
• regioneR-1.38.0 Association analysis of genomic regions based on permutation tests
• registry-0.5-1 Infrastructure for R Package Registries
• regsem-1.9.5 Regularized Structural Equation Modeling
• reldist-1.7-2 Relative Distribution Methods
• relsurv-2.2-9 Relative Survival
• remaCor-0.0.18 Random Effects Meta-Analysis for Correlated Test Statistics
• rematch-2.0.0 Match Regular Expressions with a Nicer ‘API’
• rematch2-2.1.2 Tidy Output from Regular Expression Matching
• remotes-2.5.0 R Package Installation from Remote Repositories, Including ‘GitHub’
• rentrez-1.2.3 ‘Entrez’ in R
• renv-1.0.11 Project Environments
• reprex-2.1.1 Prepare Reproducible Example Code via the Clipboard
• resample-0.6 Resampling Functions
• reshape-0.8.9 Flexibly Reshape Data
• reshape2-1.4.4 Flexibly Reshape Data: A Reboot of the Reshape Package
• restfulr-0.0.15 R Interface to RESTful Web Services
• reticulate-1.40.0 Interface to ‘Python’
• rex-1.2.1 Friendly Regular Expressions
• rgbif-3.8.1 Interface to the Global Biodiversity Information Facility API
• rgdal-1.6-7 Bindings for the ‘Geospatial’ Data Abstraction Library
• rgeos-0.6-4 Interface to Geometry Engine - Open Source (‘GEOS’)
• rgexf-0.16.3 Build, Import, and Export GEXF Graph Files
• rgl-1.3.14 3D Visualization Using OpenGL
• rhandsontable-0.3.8 Interface to the ‘Handsontable.js’ Library
• rhdf5-2.50.0 R Interface to HDF5
• rhdf5filters-1.18.0 HDF5 Compression Filters
• ridge-3.3 Ridge Regression with Automatic Selection of the Penalty Parameter
• ridigbio-0.4.1 Interface to the iDigBio Data API
• rio-1.2.3 A Swiss-Army Knife for Data I/O
• riskRegression-2023.12.21 Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks
• ritis-1.0.0 Integrated Taxonomic Information System Client
• rjson-0.2.23 JSON for R
• rlang-1.1.4 Functions for Base Types and Core R and ‘Tidyverse’ Features
• rle-0.9.2 Common Functions for Run-Length Encoded Vectors
• rlecuyer-0.3-8 R Interface to RNG with Multiple Streams
• rlemon-0.2.1 R Access to LEMON Graph Algorithms
• rlist-0.4.6.2 A Toolbox for Non-Tabular Data Manipulation
• rmarkdown-2.29 Dynamic Documents for R
• rmeta-3.0 Meta-Analysis
• rms-6.8-2 Regression Modeling Strategies
• rncl-0.8.7 An Interface to the Nexus Class Library
• rnetcarto-0.2.6 Fast Network Modularity and Roles Computation by Simulated Annealing (Rgraph C Library Wrapper for R)
• rngWELL-0.10-10 Toolbox for WELL Random Number Generators
• rngtools-1.5.2 Utility Functions for Working with Random Number Generators
• robustbase-0.99-4-1 Basic Robust Statistics
• rols-3.2.0 An R interface to the Ontology Lookup Service
• rootSolve-1.8.2.4 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations
• ropls-1.38.0 PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
• roptim-0.1.6 General Purpose Optimization in R using C++
• rotl-3.1.0 Interface to the ‘Open Tree of Life’ API
• roxygen2-7.3.2 In-Line Documentation for R
• rpact-4.1.0 Confirmatory Adaptive Clinical Trial Design and Analysis
• rpart-4.1.23 Recursive Partitioning and Regression Trees
• rpf-1.0.14 Response Probability Functions
• rprojroot-2.0.4 Finding Files in Project Subdirectories
• rrcov-1.7-6 Scalable Robust Estimators with High Breakdown Point
• rredlist-0.7.1 ‘IUCN’ Red List Client
• rsample-1.2.1 General Resampling Infrastructure
• rsconnect-1.3.3 Deploy Docs, Apps, and APIs to ‘Posit Connect’, ‘shinyapps.io’, and ‘RPubs’
• rstan-2.32.6 R Interface to Stan
• rstantools-2.4.0 Tools for Developing R Packages Interfacing with ‘Stan’
• rstatix-0.7.2 Pipe-Friendly Framework for Basic Statistical Tests
• rstudioapi-0.17.1 Safely Access the RStudio API
• rsvd-1.0.5 Randomized Singular Value Decomposition
• rtdists-0.11-5 Response Time Distributions
• rtracklayer-1.66.0 R interface to genome annotation files and the UCSC genome browser
• ruv-0.9.7.1 Detect and Remove Unwanted Variation using Negative Controls
• rversions-2.1.2 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
• rvertnet-0.8.4 Search ‘Vertnet’, a ‘Database’ of Vertebrate Specimen Records
• rvest-1.0.4 Easily Harvest (Scrape) Web Pages
• rvinecopulib-0.6.3.1.1 High Performance Algorithms for Vine Copula Modeling
• s2-1.1.7 Spherical Geometry Operators Using the S2 Geometry Library
• sampling-2.10 Survey Sampling
• samr-3.0 SAM: Significance Analysis of Microarrays
• sandwich-3.1-1 Robust Covariance Matrix Estimators
• sass-0.4.9 Syntactically Awesome Style Sheets (‘Sass’)
• scDblFinder-1.20.0 scDblFinder
• scales-1.3.0 Scale Functions for Visualization
• scam-1.2-17 Shape Constrained Additive Models
• scater-1.34.0 Single-Cell Analysis Toolkit for Gene Expression Data in R
• scattermore-1.2 Scatterplots with More Points
• scatterpie-0.2.4 Scatter Pie Plot
• scatterplot3d-0.3-44 3D Scatter Plot
• scistreer-1.2.0 Maximum-Likelihood Perfect Phylogeny Inference at Scale
• scran-1.34.0 Methods for Single-Cell RNA-Seq Data Analysis
• scrime-1.3.5 Analysis of High-Dimensional Categorical Data Such as SNP Data
• scs-3.2.4 Splitting Conic Solver
• sctransform-0.4.1 Variance Stabilizing Transformations for Single Cell UMI Data
• scuttle-1.16.0 Single-Cell RNA-Seq Analysis Utilities
• seewave-2.2.3 Sound Analysis and Synthesis
• segmented-2.1-3 Regression Models with Break-Points / Change-Points Estimation (with Possibly Random Effects)
• selectr-0.4-2 Translate CSS Selectors to XPath Expressions
• sem-3.1-16 Structural Equation Models
• semPLS-1.0-10 Structural Equation Modeling Using Partial Least Squares
• semTools-0.5-6 Useful Tools for Structural Equation Modeling
• sendmailR-1.4-0 Send Email Using R
• sensemakr-0.1.6 Sensitivity Analysis Tools for Regression Models
• sentometrics-1.0.0 An Integrated Framework for Textual Sentiment Time Series Aggregation and Prediction
• seqLogo-1.72.0 Sequence logos for DNA sequence alignments
• seqPattern-1.38.0 Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
• seqinr-4.2-36 Biological Sequences Retrieval and Analysis
• seriation-1.5.6 Infrastructure for Ordering Objects Using Seriation
• servr-0.32 A Simple HTTP Server to Serve Static Files or Dynamic Documents
• sessioninfo-1.2.2 R Session Information
• setRNG-2024.2-1 Set (Normal) Random Number Generator and Seed
• sf-1.0-19 Simple Features for R
• sfheaders-0.4.4 Converts Between R Objects and Simple Feature Objects
• sfsmisc-1.1-20 Utilities from ‘Seminar fuer Statistik’ ETH Zurich
• shadowtext-0.1.4 Shadow Text Grob and Layer
• shape-1.4.6.1 Functions for Plotting Graphical Shapes, Colors
• shapefiles-0.7.2 Read and Write ESRI Shapefiles
• shiny-1.9.1 Web Application Framework for R
• shinyBS-0.61.1 Twitter Bootstrap Components for Shiny
• shinyFiles-0.9.3 A Server-Side File System Viewer for Shiny
• shinyWidgets-0.8.7 Custom Inputs Widgets for Shiny
• shinycssloaders-1.1.0 Add Loading Animations to a ‘shiny’ Output While It’s Recalculating
• shinydashboard-0.7.2 Create Dashboards with ‘Shiny’
• shinydashboardPlus-2.0.5 Add More ‘AdminLTE2’ Components to ‘shinydashboard’
• shinyhelper-0.3.2 Easily Add Markdown Help Files to ‘shiny’ App Elements
• shinyjs-2.1.0 Easily Improve the User Experience of Your Shiny Apps in Seconds
• shinypanel-0.1.5 Shiny Control Panel
• shinystan-2.6.0 Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
• shinythemes-1.2.0 Themes for Shiny
• siggenes-1.80.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
• signal-1.8-1 Signal Processing
• simex-1.8 SIMEX- And MCSIMEX-Algorithm for Measurement Error Models
• simona-1.4.0 Semantic Similarity on Bio-Ontologies
• simplifyEnrichment-2.0.0 Simplify Functional Enrichment Results
• sitmo-2.0.2 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header Files
• slam-0.1-55 Sparse Lightweight Arrays and Matrices
• slider-0.3.2 Sliding Window Functions
• slingshot-2.14.0 Tools for ordering single-cell sequencing
• sm-2.2-6.0 Smoothing Methods for Nonparametric Regression and Density Estimation
• smoof-1.6.0.3 Single and Multi-Objective Optimization Test Functions
• smoother-1.3 Functions Relating to the Smoothing of Numerical Data
• sn-2.1.1 The Skew-Normal and Related Distributions Such as the Skew-t and the SUN
• sna-2.8 Tools for Social Network Analysis
• snow-0.4-4 Simple Network of Workstations
• snowfall-1.84-6.3 Easier Cluster Computing (Based on ‘snow’)
• snpStats-1.56.0 SnpMatrix and XSnpMatrix classes and methods
• solrium-1.2.0 General Purpose R Interface to ‘Solr’
• som-0.3-5.2 Self-Organizing Map
• soundecology-1.3.3 Soundscape Ecology
• sourcetools-0.1.7-1 Tools for Reading, Tokenizing and Parsing R Code
• sp-2.1-4 Classes and Methods for Spatial Data
• spData-2.3.3 Datasets for Spatial Analysis
• spThin-0.2.0 Functions for Spatial Thinning of Species Occurrence Records for Use in Ecological Models
• spaMM-4.5.0 Mixed-Effect Models, with or without Spatial Random Effects
• spaa-0.2.2 SPecies Association Analysis
• spacefillr-0.3.3 Space-Filling Random and Quasi-Random Sequences
• spam-2.11-0 SPArse Matrix
• sparseMatrixStats-1.18.0 Summary Statistics for Rows and Columns of Sparse Matrices
• sparsesvd-0.2-2 Sparse Truncated Singular Value Decomposition (from ‘SVDLIBC’)
• spatial-7.3-17 Functions for Kriging and Point Pattern Analysis
• spatstat-3.3-0 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
• spatstat.core-2.4-4 Core Functionality of the ‘spatstat’ Family
• spatstat.data-3.1-4 Datasets for ‘spatstat’ Family
• spatstat.explore-3.3-3 Exploratory Data Analysis for the ‘spatstat’ Family
• spatstat.geom-3.3-4 Geometrical Functionality of the ‘spatstat’ Family
• spatstat.linnet-3.2-3 Linear Networks Functionality of the ‘spatstat’ Family
• spatstat.model-3.3-3 Parametric Statistical Modelling and Inference for the ‘spatstat’ Family
• spatstat.random-3.3-2 Random Generation Functionality for the ‘spatstat’ Family
• spatstat.sparse-3.1-0 Sparse Three-Dimensional Arrays and Linear Algebra Utilities
• spatstat.univar-3.1-1 One-Dimensional Probability Distribution Support for the ‘spatstat’ Family
• spatstat.utils-3.1-1 Utility Functions for ‘spatstat’
• spdep-1.3-6 Spatial Dependence: Weighting Schemes, Statistics
• splancs-2.01-45 Spatial and Space-Time Point Pattern Analysis
• splines built in
• splitstackshape-1.4.8 Stack and Reshape Datasets After Splitting Concatenated Values
• spls-2.2-3 Sparse Partial Least Squares (SPLS) Regression and Classification
• spocc-1.2.3 Interface to Species Occurrence Data Sources
• stabledist-0.7-2 Stable Distribution Functions
• stabs-0.6-4 Stability Selection with Error Control
• stageR-1.28.0 stageR: stage-wise analysis of high throughput gene expression data in R
• stargazer-5.2.3 Well-Formatted Regression and Summary Statistics Tables
• stars-0.6-7 Spatiotemporal Arrays, Raster and Vector Data Cubes
• startupmsg-0.9.7 Utilities for Start-Up Messages
• statmod-1.5.0 Statistical Modeling
• statnet-2019.6 Software Tools for the Statistical Analysis of Network Data
• statnet.common-4.10.0 Common R Scripts and Utilities Used by the Statnet Project Software
• stats built in
• stats4 built in
• stdReg-3.4.1 Regression Standardization
• stopwords-2.3 Multilingual Stopword Lists
• stringdist-0.9.12 Approximate String Matching, Fuzzy Text Search, and String Distance Functions
• stringi-1.8.4 Fast and Portable Character String Processing Facilities
• stringmagic-1.1.2 Character String Operations and Interpolation, Magic Edition
• stringr-1.5.1 Simple, Consistent Wrappers for Common String Operations
• strucchange-1.5-4 Testing, Monitoring, and Dating Structural Changes
• struct-1.18.0 Statistics in R Using Class-based Templates
• structToolbox-1.18.0 Data processing & analysis tools for Metabolomics and other omics
• styler-1.10.3 Non-Invasive Pretty Printing of R Code
• subplex-1.9 Unconstrained Optimization using the Subplex Algorithm
• survey-4.4-2 Analysis of Complex Survey Samples
• survival-3.7-0 Survival Analysis
• survivalROC-1.0.3.1 Time-Dependent ROC Curve Estimation from Censored Survival Data
• susieR-0.12.35 Sum of Single Effects Linear Regression
• svUnit-1.0.6 ‘SciViews’ - Unit, Integration and System Testing
• sva-3.54.0 Surrogate Variable Analysis
• svd-0.5.7 Interfaces to Various State-of-Art SVD and Eigensolvers
• svglite-2.1.3 An ‘SVG’ Graphics Device
• swagger-5.17.14.1 Dynamically Generates Documentation from a ‘Swagger’ Compliant API
• symmoments-1.2.1 Symbolic Central and Noncentral Moments of the Multivariate Normal Distribution
• sys-3.4.3 Powerful and Reliable Tools for Running System Commands in R
• systemfonts-1.1.0 System Native Font Finding
• tableone-0.13.2 Create ‘Table 1’ to Describe Baseline Characteristics with or without Propensity Score Weights
• tabletools 0.1.0 Package Not Found
• tau-0.0-26 Text Analysis Utilities
• taxize-0.9.100.1 Taxonomic Information from Around the Web
• tcltk built in
• tcltk2-1.2-11 Tcl/Tk Additions
• tclust-2.0-5 Robust Trimmed Clustering
• tensor-1.5 Tensor product of arrays
• tensorA-0.36.2.1 Advanced Tensor Arithmetic with Named Indices
• tergm-4.2.1 Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models
• terra-1.7-83 Spatial Data Analysis
• testit-0.13 A Simple Package for Testing R Packages
• testthat-3.2.1.1 Unit Testing for R
• textcat-1.0-9 N-Gram Based Text Categorization
• textplot-0.2.2 Text Plots
• textshaping-0.4.0 Bindings to the ‘HarfBuzz’ and ‘Fribidi’ Libraries for Text Shaping
• threejs-0.3.3 Interactive 3D Scatter Plots, Networks and Globes
• tibble-3.2.1 Simple Data Frames
• tictoc-1.2.1 Functions for Timing R Scripts, as Well as Implementations of “Stack” and “StackList” Structures
• tidybayes-3.0.7 Tidy Data and ‘Geoms’ for Bayesian Models
• tidygraph-1.3.1 A Tidy API for Graph Manipulation
• tidyr-1.3.1 Tidy Messy Data
• tidyselect-1.2.1 Select from a Set of Strings
• tidytext-0.4.2 Text Mining using ‘dplyr’, ‘ggplot2’, and Other Tidy Tools
• tidytree-0.4.6 A Tidy Tool for Phylogenetic Tree Data Manipulation
• tidyverse-2.0.0 Easily Install and Load the ‘Tidyverse’
• tiff-0.1-12 Read and Write TIFF Images
• timeDate-4041.110 Rmetrics - Chronological and Calendar Objects
• timechange-0.3.0 Efficient Manipulation of Date-Times
• timereg-2.0.6 Flexible Regression Models for Survival Data
• tinytex-0.54 Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents
• tkWidgets-1.84.0 R based tk widgets
• tkrplot-0.0-27 TK Rplot
• tm-0.7-15 Text Mining Package
• tmap-3.3-4 Thematic Maps
• tmaptools-3.1-1 Thematic Map Tools
• tmle-2.0.1.1 Targeted Maximum Likelihood Estimation
• tmvnsim-1.0-2 Truncated Multivariate Normal Simulation
• tmvtnorm-1.6 Truncated Multivariate Normal and Student t Distribution
• tokenizers-0.3.0 Fast, Consistent Tokenization of Natural Language Text
• tools built in
• topicmodels-0.2-17 Topic Models
• tree-1.0-43 Classification and Regression Trees
• treeio-1.30.0 Base Classes and Functions for Phylogenetic Tree Input and Output
• triebeard-0.4.1 ‘Radix’ Trees in ‘Rcpp’
• trimcluster-0.1-5 Cluster Analysis with Trimming
• tripack-1.3-9.2 Triangulation of Irregularly Spaced Data
• truncnorm-1.0-9 Truncated Normal Distribution
• trust-0.1-8 Trust Region Optimization
• tseries-0.10-58 Time Series Analysis and Computational Finance
• tseriesChaos-0.1-13.1 Analysis of Nonlinear Time Series
• tsna-0.3.5 Tools for Temporal Social Network Analysis
• tsne-0.1-3.1 T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
• tuneR-1.4.7 Analysis of Music and Speech
• twang-2.6.1 Toolkit for Weighting and Analysis of Nonequivalent Groups
• tweedie-2.3.5 Evaluation of Tweedie Exponential Family Models
• tweenr-2.0.3 Interpolate Data for Smooth Animations
• txdbmaker-1.2.0 Tools for making TxDb objects from genomic annotations
• tximport-1.34.0 Import and summarize transcript-level estimates for transcript- and gene-level analysis
• tzdb-0.4.0 Time Zone Database Information
• ucminf-1.2.2 General-Purpose Unconstrained Non-Linear Optimization
• udpipe-0.8.11 Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the ‘UDPipe’ ‘NLP’ Toolkit
• umap-0.2.10.0 Uniform Manifold Approximation and Projection
• unbalanced-2.0 Racing for Unbalanced Methods Selection
• unikn-1.0.0 Graphical Elements of the University of Konstanz’s Corporate Design
• uniqueAtomMat-0.1-3-2 Finding Unique or Duplicated Rows or Columns for Atomic Matrices
• units-0.8-5 Measurement Units for R Vectors
• universalmotif-1.24.2 Import, Modify, and Export Motifs with R
• unmarked-1.4.3 Models for Data from Unmarked Animals
• urca-1.3-4 Unit Root and Cointegration Tests for Time Series Data
• urlchecker-1.0.1 Run CRAN URL Checks from Older R Versions
• urltools-1.7.3 Vectorised Tools for URL Handling and Parsing
• uroot-2.1-3 Unit Root Tests for Seasonal Time Series
• usethis-3.0.0 Automate Package and Project Setup
• utf8-1.2.4 Unicode Text Processing
• utils built in
• uuid-1.2-1 Tools for Generating and Handling of UUIDs
• uwot-0.2.2 The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction
• varhandle-2.0.6 Functions for Robust Variable Handling
• variancePartition-1.36.2 Quantify and interpret drivers of variation in multilevel gene expression experiments
• vcd-1.4-13 Visualizing Categorical Data
• vcfR-1.15.0 Manipulate and Visualize VCF Data
• vctrs-0.6.5 Vector Helpers
• vegan-2.6-8 Community Ecology Package
• venn-1.12 Draw Venn Diagrams
• vioplot-0.5.0 Violin Plot
• vipor-0.4.7 Plot Categorical Data Using Quasirandom Noise and Density Estimates
• viridis-0.6.5 Colorblind-Friendly Color Maps for R
• viridisLite-0.4.2 Colorblind-Friendly Color Maps (Lite Version)
• visNetwork-2.1.2 Network Visualization using ‘vis.js’ Library
• visdat-0.6.0 Preliminary Visualisation of Data
• vroom-1.6.5 Read and Write Rectangular Text Data Quickly
• vsn-3.74.0 Variance stabilization and calibration for microarray data
• waiter-0.2.5 Loading Screen for ‘Shiny’
• waldo-0.6.1 Find Differences Between R Objects
• warp-0.2.1 Group Dates
• wateRmelon-2.12.0 Illumina DNA methylation array normalization and metrics
• waveslim-1.8.5 Basic Wavelet Routines for One-, Two-, and Three-Dimensional Signal Processing
• wdm-0.2.4 Weighted Dependence Measures
• webshot-0.5.5 Take Screenshots of Web Pages
• webutils-1.2.2 Utility Functions for Developing Web Applications
• weights-1.0.4 Weighting and Weighted Statistics
• wellknown-0.7.4 Convert Between ‘WKT’ and ‘GeoJSON’
• whisker-0.4.1 for R, Logicless Templating
• widgetTools-1.84.0 Creates an interactive tcltk widget
• widgetframe-0.3.1 ‘Htmlwidgets’ in Responsive ‘iframes’
• wikitaxa-0.4.0 Taxonomic Information from ‘Wikipedia’
• withr-3.0.2 Run Code ‘With’ Temporarily Modified Global State
• wk-0.9.4 Lightweight Well-Known Geometry Parsing
• word2vec-0.4.0 Distributed Representations of Words
• wordcloud-2.6 Word Clouds
• worrms-0.4.3 World Register of Marine Species (WoRMS) Client
• writexl-1.5.1 Export Data Frames to Excel ‘xlsx’ Format
• xcms-4.4.0 LC-MS and GC-MS Data Analysis
• xfun-0.49 Supporting Functions for Packages Maintained by ‘Yihui Xie’
• xgboost-1.7.8.1 Extreme Gradient Boosting
• xlsx-0.6.5 Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files
• xlsxjars-0.6.1 Package required POI jars for the xlsx package
• xml2-1.3.6 Parse XML
• xopen-1.0.1 Open System Files, ‘URLs’, Anything
• xtable-1.8-4 Export Tables to LaTeX or HTML
• xts-0.14.1 eXtensible Time Series
• yaImpute-1.0-34.1 Nearest Neighbor Observation Imputation and Evaluation Tools
• yaml-2.3.10 Methods to Convert R Data to YAML and Back
• yulab.utils-0.1.8 Supporting Functions for Packages Maintained by ‘YuLab-SMU’
• zCompositions-1.5.0-4 Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
• zeallot-0.1.0 Multiple, Unpacking, and Destructuring Assignment
• zellkonverter-1.16.0 Conversion Between scRNA-seq Objects
• zip-2.3.1 Cross-Platform ‘zip’ Compression
• zlibbioc-1.52.0 An R packaged zlib-1.2.5
• zoo-1.8-12 S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations)