Known Issues
Package List
- ADGofTest-0.3 Anderson-Darling GoF test
- ALDEx2-1.22.0 Analysis Of Differential Abundance Taking Sample Variation Into Account
- ALL-1.32.0 A data package
- ASCAT 2.5.2
- AUC-0.3.0 Threshold independent performance measures for probabilistic<U+000a>classifiers.
- AgiMicroRna-2.40.0 Processing and Differential Expression Analysis of Agilent microRNA chips
- AlgDesign-1.2.0 Algorithmic Experimental Design
- AnnotationDbi-1.52.0 Manipulation of SQLite-based annotations in Bioconductor
- AnnotationFilter-1.14.0 Facilities for Filtering Bioconductor Annotation Resources
- AnnotationForge-1.32.0 Tools for building SQLite-based annotation data packages
- AnnotationHub-2.22.0 Client to access AnnotationHub resources
- BB-2019.10-1 Solving and Optimizing Large-Scale Nonlinear Systems
- BBmisc-1.11 Miscellaneous Helper Functions for B. Bischl
- BCEE-1.3.0 The Bayesian Causal Effect Estimation Algorithm
- BDgraph-2.63 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
- BH-1.72.0-3 Boost C++ Header Files
- BMA-3.18.14 Bayesian Model Averaging
- BSgenome-1.58.0 Software infrastructure for efficient representation of full genomes and their SNPs
- BSgenome.Hsapiens.UCSC.hg19-1.4.3 Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)
- BatchJobs-1.8 Batch Computing with R
- BayesPen-1.0 Bayesian Penalized Credible Regions
- BayesianTools-0.1.7 General-Purpose MCMC and SMC Samplers and Tools for Bayesian
Statistics
- Bhat-0.9-10 General likelihood exploration
- BiasedUrn-1.07 Biased Urn Model Distributions
- Biobase-2.50.0 Biobase: Base functions for Bioconductor
- BiocFileCache-1.14.0 Manage Files Across Sessions
- BiocGenerics-0.36.0 S4 generic functions used in Bioconductor
- BiocManager-1.30.10 Access the Bioconductor Project Package Repository
- BiocParallel-1.24.1 Bioconductor facilities for parallel evaluation
- BiocStyle-2.18.1 Standard styles for vignettes and other Bioconductor documents
- BiocVersion-3.12.0 Set the appropriate version of Bioconductor packages
- Biostrings-2.58.0 Efficient manipulation of biological strings
- BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
- Bolstad-0.2-41 Functions for Elementary Bayesian Inference
- Bolstad2-1.0-28 Bolstad functions
- Boruta-7.0.0 Wrapper Algorithm for All Relevant Feature Selection
- BradleyTerry2-1.1-2 Bradley-Terry Models
- Brobdingnag-1.2-6 Very Large Numbers in R
- CGHbase-1.50.0 CGHbase: Base functions and classes for arrayCGH data analysis.
- CLONETv2-2.1.0 Clonality Estimates in Tumor
- CMA-1.48.0 Synthesis of microarray-based classification
- CNEr-1.26.0 CNE Detection and Visualization
- COMPASS-1.28.0 Combinatorial Polyfunctionality Analysis of Single Cells
- CVST-0.2-2 Fast Cross-Validation via Sequential Testing
- Cairo-1.5-12.2 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-2.56.0 Category Analysis
- ChIPpeakAnno-3.24.1 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
- ComICS-1.0.4 Computational Methods for Immune Cell-Type Subsets
- CompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal Variables
- ConsensusClusterPlus-1.54.0 ConsensusClusterPlus
- CovSel-1.2.1 Model-Free Covariate Selection
- CytoML-2.2.1 A GatingML Interface for Cross Platform Cytometry Data Sharing
- DAAG-1.24 Data Analysis and Graphics Data and Functions
- DBI-1.1.0 R Database Interface
- DECIPHER-2.18.1 Tools for curating, analyzing, and manipulating biological sequences
- DEGseq-1.44.0 Identify Differentially Expressed Genes from RNA-seq data
- DESeq2-1.30.0 Differential gene expression analysis based on the negative binomial distribution
- DEoptimR-1.0-8 Differential Evolution Optimization in Pure R
- DHARMa-0.3.3.0 Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
- DNAcopy-1.64.0 DNA copy number data analysis
- DO.db-2.9 A set of annotation maps describing the entire Disease Ontology
- DOSE-3.16.0 Disease Ontology Semantic and Enrichment analysis
- DOT-0.1 Render and Export DOT Graphs in R
- DRR-0.0.4 Dimensionality Reduction via Regression
- DT-0.16 A Wrapper of the JavaScript Library ‘DataTables’
- DTRreg-1.7 DTR Estimation and Inference via G-Estimation, Dynamic WOLS,
Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
- DelayedArray-0.16.0 A unified framework for working transparently with on-disk and in-memory array-like datasets
- DelayedMatrixStats-1.12.1 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
- Deriv-4.1.2 Symbolic Differentiation
- DiagrammeR-1.0.6.1 Graph/Network Visualization
- DiceDesign-1.8-1 Designs of Computer Experiments
- DiffBind-3.0.9 Differential Binding Analysis of ChIP-Seq Peak Data
- DirichletMultinomial-1.32.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
- DiscriMiner-0.1-29 Tools of the Trade for Discriminant Analysis
- DistributionUtils-0.6-0 Distribution Utilities
- DynDoc-1.68.0 Dynamic document tools
- EBImage-4.32.0 Image processing and analysis toolbox for R
- EasyABC-1.5 Efficient Approximate Bayesian Computation Sampling Schemes
- EpiModel-2.0.3 Mathematical Modeling of Infectious Disease Dynamics
- FDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probes
- FME-1.3.6.1 A Flexible Modelling Environment for Inverse Modelling,
Sensitivity, Identifiability and Monte Carlo Analysis
- FNN-1.1.3 Fast Nearest Neighbor Search Algorithms and Applications
- FactoMineR-2.4 Multivariate Exploratory Data Analysis and Data Mining
- FlowSOM-1.22.0 Using self-organizing maps for visualization and interpretation of cytometry data
- Formula-1.2-4 Extended Model Formulas
- GENESIS-2.20.0 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
- GEOquery-2.58.0 Get data from NCBI Gene Expression Omnibus (GEO)
- GGally-2.0.0 Extension to ‘ggplot2’
- GO.db-3.12.1 A set of annotation maps describing the entire Gene Ontology
- GOSemSim-2.16.1 GO-terms Semantic Similarity Measures
- GOstats-2.56.0 Tools for manipulating GO and microarrays
- GPfit-1.0-8 Gaussian Processes Modeling
- GSA-1.03.1 Gene Set Analysis
- GSEABase-1.52.1 Gene set enrichment data structures and methods
- GSVA-1.38.0 Gene Set Variation Analysis for microarray and RNA-seq data
- GUTS-1.1.1 Fast Calculation of the Likelihood of a Stochastic Survival
Model
- GWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association Studies
- GWASTools-1.36.0 Tools for Genome Wide Association Studies
- GenSA-1.1.7 Generalized Simulated Annealing
- GeneNet-1.2.15 Modeling and Inferring Gene Networks
- GenomeGraphs 1.46.0
- GenomeInfoDb-1.26.2 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
- GenomeInfoDbData-1.2.4 Species and taxonomy ID look up tables used by GenomeInfoDb
- GenomicAlignments-1.26.0 Representation and manipulation of short genomic alignments
- GenomicFeatures-1.42.1 Conveniently import and query gene models
- GenomicFiles-1.26.0 Distributed computing by file or by range
- GenomicRanges-1.42.0 Representation and manipulation of genomic intervals
- GetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable Interpolation
- GillespieSSA-0.6.1 Gillespie’s Stochastic Simulation Algorithm (SSA)
- Glimma-2.0.0 Interactive HTML graphics
- GlobalOptions-0.1.2 Generate Functions to Get or Set Global Options
- Gmisc-1.11.0 Descriptive Statistics, Transition Plots, and More
- GreyListChIP-1.22.0 Grey Lists – Mask Artefact Regions Based on ChIP Inputs
- Gviz-1.34.0 Plotting data and annotation information along genomic coordinates
- HCsnip 1.2.0
- HDF5Array-1.18.0 HDF5 backend for DelayedArray objects
- HMMcopy-1.32.0 Copy number prediction with correction for GC and mappability bias for HTS data
- HSMMSingleCell-1.10.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)
- HaploSim-1.8.4 Functions to simulate haplotypes
- HiddenMarkov-1.8-11 Hidden Markov Models
- Hmisc-4.4-2 Harrell Miscellaneous
- Homo.sapiens-1.3.1 Annotation package for the Homo.sapiens object
- IDPmisc-1.1.20 ‘Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)’
- IDSpatialStats-0.3.10 Estimate Global Clustering in Infectious Disease
- IHW-1.18.0 Independent Hypothesis Weighting
- IRanges-2.24.1 Foundation of integer range manipulation in Bioconductor
- IRdisplay-0.7.0 ‘Jupyter’ Display Machinery
- ISOcodes-2020.12.04 Selected ISO Codes
- IlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arrays
- Iso-0.0-18.1 Functions to Perform Isotonic Regression
- JBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J.
Buttlar
- KEGG.db-3.2.4 A set of annotation maps for KEGG
- KEGGREST-1.30.1 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
- KEGGgraph-1.50.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
- KEGGprofile-1.32.0 An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway
- KODAMA-1.5 Knowledge Discovery by Accuracy Maximization
- KernSmooth-2.23-18 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
- LaplacesDemon-16.1.4 Complete Environment for Bayesian Inference
- LearnBayes-2.15.1 Functions for Learning Bayesian Inference
- Lmoments-1.3-1 L-Moments and Quantile Mixtures
- LogicReg-1.6.2 Logic Regression
- LymphoSeq-1.18.0 Analyze high-throughput sequencing of T and B cell receptors
- LymphoSeqDB-0.99.2 LymphoSeq annotation databases
- MAGeCKFlute-1.10.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
- MALDIquant-1.19.3 Quantitative Analysis of Mass Spectrometry Data
- MASS-7.3-53 Support Functions and Datasets for Venables and Ripley’s MASS
- MAST-1.16.0 Model-based Analysis of Single Cell Transcriptomics
- MCMCglmm-2.29 MCMC Generalised Linear Mixed Models
- MCMCpack-1.4-9 Markov Chain Monte Carlo (MCMC) Package
- MIIVsem-0.5.5 Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
- MPV-1.55 Data Sets from Montgomery, Peck and Vining
- MatchIt-4.1.0 Nonparametric Preprocessing for Parametric Causal Inference
- Matching-4.9-7 Multivariate and Propensity Score Matching with Balance
Optimization
- Matrix-1.2-18 Sparse and Dense Matrix Classes and Methods
- MatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
Operations
- MatrixGenerics-1.2.0 S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
- MatrixModels-0.4-1 Modelling with Sparse And Dense Matrices
- Mfuzz-2.50.0 Soft clustering of time series gene expression data
- ModelMetrics-1.2.2.2 Rapid Calculation of Model Metrics
- NADA-1.6-1.1 Nondetects and Data Analysis for Environmental Data
- NLP-0.2-1 Natural Language Processing Infrastructure
- NOISeq-2.34.0 Exploratory analysis and differential expression for RNA-seq data
- OceanView-1.0.5 Visualisation of Oceanographic Data and Model Output
- OrganismDbi-1.32.0 Software to enable the smooth interfacing of different database packages
- PBSddesolve-1.12.6 Solver for Delay Differential Equations
- PFAM.db-3.12.0 A set of protein ID mappings for PFAM
- PICS-2.34.0 Probabilistic inference of ChIP-seq
- PKI-0.1-7 Public Key Infrastucture for R Based on the X.509 Standard
- ParamHelpers-1.14 Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning
- PoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log
linear model
- PolynomF-2.0-3 Polynomials in R
- PresenceAbsence-1.1.9 Presence-Absence Model Evaluation.
- ProtGenerics-1.22.0 S4 generic functions for Bioconductor proteomics infrastructure
- QUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix Estimation
- R.cache-0.14.0 Fast and Light-Weight Caching (Memoization) of Objects and
Results to Speed Up Computations
- R.matlab-3.6.2 Read and Write MAT Files and Call MATLAB from Within R
- R.methodsS3-1.8.1 S3 Methods Simplified
- R.oo-1.24.0 R Object-Oriented Programming with or without References
- R.rsp-0.44.0 Dynamic Generation of Scientific Reports
- R.utils-2.10.1 Various Programming Utilities
- R2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
- R2jags-0.6-1 Using R to Run ‘JAGS’
- R6-2.5.0 Encapsulated Classes with Reference Semantics
- RANN-2.6.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
Metric
- RBGL-1.66.0 An interface to the BOOST graph library
- RCircos-1.2.1 Circos 2D Track Plot
- RColorBrewer-1.1-2 ColorBrewer Palettes
- RCurl-1.98-1.2 General Network (HTTP/FTP/…) Client Interface for R
- REDCapR-0.11.0 Interaction Between R and REDCap
- RGCCA-2.1.2 Regularized and Sparse Generalized Canonical Correlation
Analysis for Multiblock Data
- RInside-0.2.16 C++ Classes to Embed R in C++ (and C) Applications
- RItools-0.1-17 Randomization Inference Tools
- RJSONIO-1.3-1.4 Serialize R Objects to JSON, JavaScript Object Notation
- RLRsim-3.1-6 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
Models
- RMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix<U+000a>Theory
- RNASeqPower-1.30.0 Sample size for RNAseq studies
- RNeXML-2.4.5 Semantically Rich I/O for the ‘NeXML’ Format
- RNifti-1.3.0 Fast R and C++ Access to NIfTI Images
- ROCR-1.0-11 Visualizing the Performance of Scoring Classifiers
- ROI-1.0-0 R Optimization Infrastructure
- ROI.plugin.glpk-1.0-0 ‘ROI’ Plug-in ‘GLPK’
- RPresto-1.3.5 DBI Connector to Presto
- RProtoBufLib-2.2.0 C++ headers and static libraries of Protocol buffers
- RSNNS-0.4-12 Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)
- RSQLite-2.2.1 ‘SQLite’ Interface for R
- RSclient-0.7-3 Client for Rserve
- RSpectra-0.16-0 Solvers for Large-Scale Eigenvalue and SVD Problems
- RUnit-0.4.32 R Unit Test Framework
- RWeka-0.4-43 R/Weka Interface
- RWekajars-3.9.3-2 R/Weka Interface Jars
- Rborist-0.2-3 Extensible, Parallelizable Implementation of the Random Forest
Algorithm
- Rcpp-1.0.5 Seamless R and C++ Integration
- RcppAnnoy-0.0.18 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
Neighbors
- RcppArmadillo-0.10.1.2.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra
Library
- RcppCCTZ-0.2.9 ‘Rcpp’ Bindings for the ‘CCTZ’ Library
- RcppDate-0.0.1 ‘date’ C++ Header Library for Date and Time Functionality
- RcppEigen-0.3.3.7.0 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra
Library
- RcppGSL-0.3.8 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and Matrices
- RcppNumerical-0.4-0 ‘Rcpp’ Integration for Numerical Computing Libraries
- RcppParallel-5.0.2 Parallel Programming Tools for ‘Rcpp’
- RcppProgress-0.4.2 An Interruptible Progress Bar with OpenMP Support for C++ in R
Packages
- RcppRoll-0.3.0 Efficient Rolling / Windowed Operations
- Rdpack-2.1 Update and Manipulate Rd Documentation Objects
- Rdsdp-1.0.5 R Interface to DSDP Semidefinite Programming Library
- ReportingTools-2.30.0 Tools for making reports in various formats
- Rglpk-0.6-4 R/GNU Linear Programming Kit Interface
- Rgraphviz-2.34.0 Provides plotting capabilities for R graph objects
- Rhdf5lib-1.12.0 hdf5 library as an R package
- Rhpc-0.19-276 Permits *apply() Style Dispatch for ‘HPC’
- Rhtslib-1.22.0 HTSlib high-throughput sequencing library as an R package
- Ringo-1.54.0 R Investigation of ChIP-chip Oligoarrays
- Rlabkey-2.5.5 Data Exchange Between R and ‘LabKey’ Server
- Rmpi-0.6-9 Interface (Wrapper) to MPI (Message-Passing Interface)
- Rook-1.1-1 Rook - a web server interface for R
- Rsamtools-2.6.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
- Rserve-1.7-3.1 Binary R server
- Rssa-1.0.3 A Collection of Methods for Singular Spectrum Analysis
- Rsubread-2.4.2 Mapping, quantification and variant analysis of sequencing data
- Rtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
Implementation
- Rttf2pt1-1.3.8 ‘ttf2pt1’ Program
- S4Vectors-0.28.1 Foundation of vector-like and list-like containers in Bioconductor
- SDMTools-1.1-221.2 Species Distribution Modelling Tools: Tools for processing data
associated with species distribution modelling exercises
- SKAT-2.0.1 SNP-Set (Sequence) Kernel Association Test
- SNPRelate-1.24.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
- SNPassoc-2.0-2 SNPs-Based Whole Genome Association Studies
- 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-2.42.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
- SQUAREM-2020.5 Squared Extrapolation Methods for Accelerating EM-Like Monotone
Algorithms
- SemiPar-1.0-4.2 Semiparametic Regression
- SeqArray-1.30.0 Data management of large-scale whole-genome sequence variant calls
- SeqVarTools-1.28.1 Tools for variant data
- Seurat-3.2.3 Tools for Single Cell Genomics
- ShortRead-1.48.0 FASTQ input and manipulation
- SignifReg-3.0 Consistent Significance Controlled Variable Selection in Linear
Regression
- SimSeq-1.4.0 Nonparametric Simulation of RNA-Seq Data
- SingleCellExperiment-1.12.0 S4 Classes for Single Cell Data
- SnowballC-0.7.0 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 Library
- SparseM-1.78 Sparse Linear Algebra
- StanHeaders-2.21.0-6 C++ Header Files for Stan
- SummarizedExperiment-1.20.0 SummarizedExperiment container
- SuperLearner-2.0-26 Super Learner Prediction
- SuppDists-1.1-9.5 Supplementary Distributions
- TFBSTools-1.28.0 Software Package for Transcription Factor Binding Site (TFBS) Analysis
- TFMPvalue-0.0.8 Efficient and Accurate P-Value Computation for Position Weight
Matrices
- TFisher-0.2.0 Optimal Thresholding Fisher’s P-Value Combination Method
- TH.data-1.0-10 TH’s Data Archive
- TMB-1.7.18 Template Model Builder: A General Random Effect Tool Inspired by
‘ADMB’
- TTR-0.24.2 Technical Trading Rules
- TeachingDemos-2.12 Demonstrations for Teaching and Learning
- TitanCNA-1.28.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
- TraMineR-2.2-1 Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
- TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)
- UpSetR-1.4.0 A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
- V8-3.4.0 Embedded JavaScript and WebAssembly Engine for R
- VGAM-1.1-4 Vector Generalized Linear and Additive Models
- VIM-6.0.0 Visualization and Imputation of Missing Values
- VSURF-1.1.0 Variable Selection Using Random Forests
- VariantAnnotation-1.36.0 Annotation of Genetic Variants
- VennDiagram-1.6.20 Generate High-Resolution Venn and Euler Plots
- WeightSVM-1.7-5 Subject Weighted Support Vector Machines
- WikidataR-1.4.0 API Client Library for ‘Wikidata’
- WikipediR-1.5.0 A MediaWiki API Wrapper
- Wrench-1.8.0 Wrench normalization for sparse count data
- WriteXLS-6.1.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) Files
- XML-3.99-0.5 Tools for Parsing and Generating XML Within R and S-Plus
- XVector-0.30.0 Foundation of external vector representation and manipulation in Bioconductor
- abc-2.1 Tools for Approximate Bayesian Computation (ABC)
- abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)
- abe-3.0.1 Augmented Backward Elimination
- abind-1.4-5 Combine Multidimensional Arrays
- acepack-1.4.1 ACE and AVAS for Selecting Multiple Regression Transformations
- adabag-4.2 Applies Multiclass AdaBoost.M1, SAMME and Bagging
- ade4-1.7-16 Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
- admisc-0.11 Adrian Dusa’s Miscellaneous
- affy-1.68.0 Methods for Affymetrix Oligonucleotide Arrays
- affycoretools-1.62.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
- affyio-1.60.0 Tools for parsing Affymetrix data files
- aggregation-1.0.1 p-Value Aggregation Methods
- akima-0.6-2.1 Interpolation of Irregularly and Regularly Spaced Data
- alr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Edition
- amap-0.8-18 Another Multidimensional Analysis Package
- animation-2.6 A Gallery of Animations in Statistics and Utilities to Create
Animations
- annaffy-1.62.0 Annotation tools for Affymetrix biological metadata
- annotate-1.68.0 Annotation for microarrays
- aod-1.3.1 Analysis of Overdispersed Data
- ape-5.4-1 Analyses of Phylogenetics and Evolution
- apeglm-1.12.0 Approximate posterior estimation for GLM coefficients
- aplot-0.0.6 Decorate a ‘ggplot’ with Associated Information
- argparse-2.0.3 Command Line Optional and Positional Argument Parser
- argparser-0.6 Command-Line Argument Parser
- arm-1.11-2 Data Analysis Using Regression and Multilevel/Hierarchical
Models
- arsenal-3.5.0 An Arsenal of ‘R’ Functions for Large-Scale Statistical
Summaries
- arules-1.6-6 Mining Association Rules and Frequent Itemsets
- ash-1.0-15 David Scott’s ASH Routines
- ashr-2.2-47 Methods for Adaptive Shrinkage, using Empirical Bayes
- askpass-1.1 Safe Password Entry for R, Git, and SSH
- asnipe-1.1.13 Animal Social Network Inference and Permutations for Ecologists
- assertthat-0.2.1 Easy Pre and Post Assertions
- audio-0.1-7 Audio Interface for R
- 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
- backports-1.2.1 Reimplementations of Functions Introduced Since R-3.0.0
- bacr-1.0.1 Bayesian Adjustment for Confounding
- bamsignals-1.22.0 Extract read count signals from bam files
- bartMachine-1.2.5.1 Bayesian Additive Regression Trees
- bartMachineJARs-1.1 bartMachine JARs
- base built in
- base64-2.0 Base64 Encoder and Decoder
- base64enc-0.1-3 Tools for base64 encoding
- base64url-1.4 Fast and URL-Safe Base64 Encoder and Decoder
- batchtools-0.9.14 Tools for Computation on Batch Systems
- baySeq-2.24.0 Empirical Bayesian analysis of patterns of differential expression in count data
- bayesm-3.1-4 Bayesian Inference for Marketing/Micro-Econometrics
- bayesplot-1.7.2 Plotting for Bayesian Models
- bbmle-1.0.23.1 Tools for General Maximum Likelihood Estimation
- bdsmatrix-1.3-4 Routines for Block Diagonal Symmetric Matrices
- beanplot-1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin<U+000a>Plot)
- beeswarm-0.2.3 The Bee Swarm Plot, an Alternative to Stripchart
- benchmark-0.3-6 Benchmark Experiments Toolbox
- bezier-1.1.2 Toolkit for Bezier Curves and Splines
- bibtex-0.4.2.3 Bibtex Parser
- biglm-0.9-2.1 Bounded Memory Linear and Generalized Linear Models
- bigmemory-4.5.36 Manage Massive Matrices with Shared Memory and Memory-Mapped
Files
- bigmemory.sri-0.1.3 A shared resource interface for Bigmemory Project packages
- bindr-0.1.1 Parametrized Active Bindings
- bindrcpp-0.2.2 An ‘Rcpp’ Interface to Active Bindings
- bio3d-2.4-1 Biological Structure Analysis
- biom-0.3.12 An interface package (beta) for the BIOM file format.
- biomaRt-2.46.0 Interface to BioMart databases (i.e. Ensembl)
- biomformat-1.18.0 An interface package for the BIOM file format
- biovizBase-1.38.0 Basic graphic utilities for visualization of genomic data.
- bit-4.0.4 Classes and Methods for Fast Memory-Efficient Boolean Selections
- bit64-4.0.5 A S3 Class for Vectors of 64bit Integers
- bitops-1.0-6 Bitwise Operations
- blob-1.2.1 A Simple S3 Class for Representing Vectors of Binary Data
(‘BLOBS’)
- bmp-0.3 Read Windows Bitmap (BMP) Images
- bnlearn-4.6.1 Bayesian Network Structure Learning, Parameter Learning and
Inference
- bold-1.1.0 Interface to Bold Systems API
- bookdown-0.21 Authoring Books and Technical Documents with R Markdown
- boot-1.3-25 Bootstrap Functions (Originally by Angelo Canty for S)
- bootstrap-2019.6 Functions for the Book “An Introduction to the Bootstrap”
- breakaway-3.0 Species Richness Estimation and Modeling
- brew-1.0-6 Templating Framework for Report Generation
- brglm-0.7.1 Bias Reduction in Binomial-Response Generalized Linear Models
- bridgedist-0.1.0 An Implementation of the Bridge Distribution with Logit-Link as
in Wang and Louis (2003)
- bridgesampling-1.0-0 Bridge Sampling for Marginal Likelihoods and Bayes Factors
- brio-1.1.0 Basic R Input Output
- broom-0.7.3 Convert Statistical Objects into Tidy Tibbles
- bst-0.3-23 Gradient Boosting
- bumphunter-1.32.0 Bump Hunter
- caTools-1.18.0 Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
- cachem-1.0.1 Cache R Objects with Automatic Pruning
- calibrate-1.7.7 Calibration of Scatterplot and Biplot Axes
- callr-3.5.1 Call R from R
- car-3.0-10 Companion to Applied Regression
- carData-3.0-4 Companion to Applied Regression Data Sets
- caret-6.0-86 Classification and Regression Training
- catdata-1.2.2 Categorical Data
- 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.
- checkmate-2.0.0 Fast and Versatile Argument Checks
- chemometrics-1.4.2 Multivariate Statistical Analysis in Chemometrics
- chipseq-1.40.0 chipseq: A package for analyzing chipseq data
- chromVAR-1.12.0 Chromatin Variation Across Regions
- chron-2.3-56 Chronological Objects which can Handle Dates and Times
- circlize-0.4.11 Circular Visualization
- circular-0.4-93 Circular Statistics
- clValid-0.6-9 Validation of Clustering Results
- class-7.3-17 Functions for Classification
- classInt-0.4-3 Choose Univariate Class Intervals
- cli-2.2.0 Helpers for Developing Command Line Interfaces
- clipr-0.7.1 Read and Write from the System Clipboard
- clisymbols-1.2.0 Unicode Symbols at the R Prompt
- clue-0.3-58 Cluster Ensembles
- cluster-2.1.0 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et
al.
- clusterGeneration-1.3.7 Random Cluster Generation (with Specified Degree of Separation)
- clusterProfiler-3.18.0 statistical analysis and visualization of functional profiles for genes and gene clusters
- clusterRepro-0.9 Reproducibility of Gene Expression Clusters
- clustree-0.4.3 Visualise Clusterings at Different Resolutions
- cobs-1.3-4 Constrained B-Splines (Sparse Matrix Based)
- coda-0.19-4 Output Analysis and Diagnostics for MCMC
- codetools-0.2-18 Code Analysis Tools for R
- coin-1.3-1 Conditional Inference Procedures in a Permutation Test Framework
- colorspace-2.0-0 A Toolbox for Manipulating and Assessing Colors and Palettes
- colourpicker-1.1.0 A Colour Picker Tool for Shiny and for Selecting Colours in
Plots
- combinat-0.0-8 combinatorics utilities
- commonmark-1.7 High Performance CommonMark and Github Markdown Rendering in R
- compare-0.2-6 Comparing Objects for Differences
- compositions-2.0-0 Compositional Data Analysis
- conditionz-0.1.0 Control How Many Times Conditions are Thrown
- config-0.3.1 Manage Environment Specific Configuration Values
- conquer-1.0.2 Convolution-Type Smoothed Quantile Regression
- copula-1.0-1 Multivariate Dependence with Copulas
- copynumber-1.30.0 Segmentation of single- and multi-track copy number data by penalized least squares regression.
- corpcor-1.6.9 Efficient Estimation of Covariance and (Partial) Correlation
- corrplot-0.84 Visualization of a Correlation Matrix
- covr-3.5.1 Test Coverage for Packages
- cowplot-1.1.0 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’
- coxme-2.2-16 Mixed Effects Cox Models
- cpp11-0.2.4 A C++11 Interface for R’s C Interface
- crayon-1.3.4 Colored Terminal Output
- credentials-1.3.0 Tools for Managing SSH and Git Credentials
- crosstalk-1.1.0.1 Inter-Widget Interactivity for HTML Widgets
- crul-1.0.0 HTTP Client
- csSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarrays
- ctmle-0.1.2 Collaborative Targeted Maximum Likelihood Estimation
- cubature-2.0.4.1 Adaptive Multivariate Integration over Hypercubes
- cummeRbund-2.32.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
- curl-4.3 A Modern and Flexible Web Client for R
- cvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervals
- cyclocomp-1.1.0 Cyclomatic Complexity of R Code
- cytolib-2.2.0 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
- dada2-1.18.0 Accurate, high-resolution sample inference from amplicon sequencing data
- data.table-1.13.4 Extension of
data.frame
- datasets built in
- dbplyr-2.0.0 A ‘dplyr’ Back End for Databases
- ddalpha-1.3.11 Depth-Based Classification and Calculation of Data Depth
- deSolve-1.28 Solvers for Initial Value Problems of Differential Equations
(‘ODE’, ‘DAE’, ‘DDE’)
- deal-1.2-39 Learning Bayesian Networks with Mixed Variables
- debugme-1.1.0 Debug R Packages
- degreenet-1.3-3 Models for Skewed Count Distributions Relevant to Networks
- deldir-0.2-3 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
- dendextend-1.14.0 Extending ‘dendrogram’ Functionality in R
- derfinder-1.24.2 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
- derfinderHelper-1.24.1 derfinder helper package
- desc-1.2.0 Manipulate DESCRIPTION Files
- descr-1.1.4 Descriptive Statistics
- devtools-2.3.2 Tools to Make Developing R Packages Easier
- dfidx-0.0-3 Indexed Data Frames
- dfoptim-2020.10-1 Derivative-Free Optimization
- diagram-1.6.5 Functions for Visualising Simple Graphs (Networks), Plotting
Flow Diagrams
- dials-0.0.9 Tools for Creating Tuning Parameter Values
- diamonds-1.0-5 Analysis and sampling grids from diamond partitions
- dichromat-2.0-0 Color Schemes for Dichromats
- diffobj-0.3.2 Diffs for R Objects
- diffusionMap-1.2.0 Diffusion Map
- digest-0.6.27 Create Compact Hash Digests of R Objects
- dimRed-0.2.3 A Framework for Dimensionality Reduction
- diptest-0.75-7 Hartigan’s Dip Test Statistic for Unimodality - Corrected
- dismo-1.3-3 Species Distribution Modeling
- distillery-1.2 Method Functions for Confidence Intervals and to Distill
Information from an Object
- distr-2.8.0 Object Oriented Implementation of Distributions
- distrEx-2.8.0 Extensions of Package ‘distr’
- diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis
Package
- doBy-4.6.8 Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
- doMC-1.3.7 Foreach Parallel Adaptor for ‘parallel’
- doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
- doParallel-1.0.16 Foreach Parallel Adaptor for the ‘parallel’ Package
- doRNG-1.8.2 Generic Reproducible Parallel Backend for ‘foreach’ Loops
- doSNOW-1.0.19 Foreach Parallel Adaptor for the ‘snow’ Package
- dotCall64-1.0-0 Enhanced Foreign Function Interface Supporting Long Vectors
- downloader-0.4 Download Files over HTTP and HTTPS
- dplyr-1.0.2 A Grammar of Data Manipulation
- dqrng-0.2.1 Fast Pseudo Random Number Generators
- dr-3.0.10 Methods for Dimension Reduction for Regression
- dtangle-2.0.9 Cell Type Deconvolution from Gene Expressions
- dtw-1.22-3 Dynamic Time Warping Algorithms
- dummies-1.5.6 Create dummy/indicator variables flexibly and efficiently
- 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
- e1071-1.7-4 Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
- edgeR-3.32.0 Empirical Analysis of Digital Gene Expression Data in R
- elasticnet-1.3 Elastic-Net for Sparse Estimation and Sparse PCA
- ellipse-0.4.2 Functions for Drawing Ellipses and Ellipse-Like Confidence
Regions
- ellipsis-0.3.1 Tools for Working with …
- emdbook-1.3.12 Support Functions and Data for “Ecological Models and Data”
- emulator-1.2-20 Bayesian Emulation of Computer Programs
- energy-1.7-7 E-Statistics: Multivariate Inference via the Energy of Data
- enrichplot-1.10.1 Visualization of Functional Enrichment Result
- ensembldb-2.14.0 Utilities to create and use Ensembl-based annotation databases
- entropy-1.2.1 Estimation of Entropy, Mutual Information and Related Quantities
- epitools-0.5-10.1 Epidemiology Tools
- ergm-3.11.0 Fit, Simulate and Diagnose Exponential-Family Models for
Networks
- ergm.count-3.4.0 Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edges
- etrunct-0.1 Computes Moments of Univariate Truncated t Distribution
- europepmc-0.4 R Interface to the Europe PubMed Central RESTful Web Service
- evaluate-0.14 Parsing and Evaluation Tools that Provide More Details than the
Default
- expm-0.999-5 Matrix Exponential, Log, ‘etc’
- expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
- extRemes-2.1 Extreme Value Analysis
- extrafont-0.17 Tools for using fonts
- extrafontdb-1.0 Package for holding the database for the extrafont package
- fail-1.3 File Abstraction Interface Layer (FAIL)
- fansi-0.4.1 ANSI Control Sequence Aware String Functions
- faraway-1.0.7 Functions and Datasets for Books by Julian Faraway
- farver-2.0.3 High Performance Colour Space Manipulation
- fastICA-1.2-2 FastICA Algorithms to Perform ICA and Projection Pursuit
- fastcluster-1.1.25 Fast Hierarchical Clustering Routines for R and ‘Python’
- fastmap-1.0.1 Fast Data Structures
- fastmatch-1.1-0 Fast match() function
- fastseg-1.36.0 fastseg - a fast segmentation algorithm
- fasttime-1.0-2 Fast Utility Function for Time Parsing and Conversion
- fda-5.1.9 Functional Data Analysis
- fdrtool-1.2.15 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’
- ff-4.0.4 Memory-Efficient Storage of Large Data on Disk and Fast Access
Functions
- ffbase-0.13.1 Basic Statistical Functions for Package ‘ff’
- fftw-1.0-6 Fast FFT and DCT Based on the FFTW Library
- fftwtools-0.9-9 Wrapper for ‘FFTW3’ Includes: One-Dimensional Univariate,
One-Dimensional Multivariate, and Two-Dimensional Transform
- fgsea-1.16.0 Fast Gene Set Enrichment Analysis
- fields-11.6 Tools for Spatial Data
- filehash-2.4-2 Simple Key-Value Database
- findpython-1.0.5 Functions to Find an Acceptable Python Binary
- fishMod-0.29 Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta
Log-Normal Models
- fit.models-0.64 Compare Fitted Models
- fitdistrplus-1.1-3 Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
- flashClust-1.01-2 Implementation of optimal hierarchical clustering
- flexclust-1.4-0 Flexible Cluster Algorithms
- flexmix-2.3-17 Flexible Mixture Modeling
- flowClust-3.28.0 Clustering for Flow Cytometry
- flowCore-2.2.0 flowCore: Basic structures for flow cytometry data
- flowStats-4.2.0 Statistical methods for the analysis of flow cytometry data
- flowViz-1.54.0 Visualization for flow cytometry
- flowWorkspace-4.2.0 Infrastructure for representing and interacting with gated and ungated cytometry data sets.
- fma-2.4 Data Sets from “Forecasting: Methods and Applications” by
Makridakis, Wheelwright & Hyndman (1998)
- forcats-0.5.0 Tools for Working with Categorical Variables (Factors)
- foreach-1.5.1 Provides Foreach Looping Construct
- forecast-8.13 Forecasting Functions for Time Series and Linear Models
- foreign-0.8-80 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’,
‘Systat’, ‘Weka’, ‘dBase’, …
- forestplot-1.10.1 Advanced Forest Plot Using ‘grid’ Graphics
- forge-0.2.0 Casting Values into Shape
- formatR-1.7 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-2.2-9 Flexible Procedures for Clustering
- fpp-0.5 Data for “Forecasting: principles and practice”
- fracdiff-1.5-1 Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models
- fs-1.5.0 Cross-Platform File System Operations Based on ‘libuv’
- fts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)
- furrr-0.2.1 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-1.21.0 Unified Parallel and Distributed Processing in R for Everyone
- future.apply-1.7.0 Apply Function to Elements in Parallel using Futures
- gage-2.40.1 Generally Applicable Gene-set Enrichment for Pathway Analysis
- gam-1.20 Generalized Additive Models
- gamlss-5.2-0 Generalised Additive Models for Location Scale and Shape
- gamlss.data-5.1-4 GAMLSS Data
- gamlss.dist-5.1-7 Distributions for Generalized Additive Models for Location Scale
and Shape
- gamlss.tr-5.1-7 Generating and Fitting Truncated `gamlss.family’ Distributions
- gamm4-0.2-6 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’
- gap-1.2.2 Genetic Analysis Package
- gapfill-0.9.6 Fill Missing Values in Satellite Data
- gbRd-0.4-11 Utilities for processing Rd objects and files
- gbm-2.1.8 Generalized Boosted Regression Models
- gclus-1.3.2 Clustering Graphics
- gcrma-2.62.0 Background Adjustment Using Sequence Information
- gdata-2.18.0 Various R Programming Tools for Data Manipulation
- gdistance-1.3-6 Distances and Routes on Geographical Grids
- gdsfmt-1.26.1 R Interface to CoreArray Genomic Data Structure (GDS) files
- gdtools-0.2.2 Utilities for Graphical Rendering
- gee-4.13-20 Generalized Estimation Equation Solver
- geepack-1.3-1 Generalized Estimating Equation Package
- geiger-2.0.7 Analysis of Evolutionary Diversification
- geneLenDataBase-1.26.0 Lengths of mRNA transcripts for a number of genomes
- genefilter-1.72.0 genefilter: methods for filtering genes from high-throughput experiments
- geneplotter-1.68.0 Graphics related functions for Bioconductor
- generics-0.1.0 Common S3 Generics not Provided by Base R Methods Related to
Model Fitting
- genoset-1.45.1 A RangedSummarizedExperiment with methods for copy number analysis
- geometry-0.4.5 Mesh Generation and Surface Tessellation
- gert-1.0.2 Simple Git Client for R
- getopt-1.20.3 C-Like ‘getopt’ Behavior
- ggExtra-0.9 Add Marginal Histograms to ‘ggplot2’, and More ‘ggplot2’
Enhancements
- ggbeeswarm-0.6.0 Categorical Scatter (Violin Point) Plots
- ggbio-1.38.0 Visualization tools for genomic data
- ggcyto-1.18.0 Visualize Cytometry data with ggplot
- ggdendro-0.1.22 Create Dendrograms and Tree Diagrams Using ‘ggplot2’
- ggforce-0.3.2 Accelerating ‘ggplot2’
- ggplot2-3.3.3 Create Elegant Data Visualisations Using the Grammar of Graphics
- ggplotify-0.0.5 Convert Plot to ‘grob’ or ‘ggplot’ Object
- ggpubr-0.4.0 ‘ggplot2’ Based Publication Ready Plots
- ggraph-2.0.4 An Implementation of Grammar of Graphics for Graphs and Networks
- ggrepel-0.9.0 Automatically Position Non-Overlapping Text Labels with
‘ggplot2’
- ggridges-0.5.2 Ridgeline Plots in ‘ggplot2’
- ggsci-2.9 Scientific Journal and Sci-Fi Themed Color Palettes for
‘ggplot2’
- ggsignif-0.6.0 Significance Brackets for ‘ggplot2’
- ggthemes-4.2.0 Extra Themes, Scales and Geoms for ‘ggplot2’
- ggtree-2.4.1 an R package for visualization of tree and annotation data
- ggvis-0.4.7 Interactive Grammar of Graphics
- gh-1.2.0 ‘GitHub’ ‘API’
- git2r-0.27.1 Provides Access to Git Repositories
- gitcreds-0.1.1 Query ‘git’ Credentials from ‘R’
- glasso-1.11 Graphical Lasso: Estimation of Gaussian Graphical Models
- gllvm-1.2.3 Generalized Linear Latent Variable Models
- glmmML-1.1.1 Generalized Linear Models with Clustering
- glmmTMB-1.0.2.1 Generalized Linear Mixed Models using Template Model Builder
- glmnet-4.0-2 Lasso and Elastic-Net Regularized Generalized Linear Models
- glmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox
Proportional Hazards Model
- globals-0.14.0 Identify Global Objects in R Expressions
- glue-1.4.2 Interpreted String Literals
- gmm-1.6-5 Generalized Method of Moments and Generalized Empirical
Likelihood
- gmodels-2.18.1 Various R Programming Tools for Model Fitting
- gmp-0.6-1 Multiple Precision Arithmetic
- goftest-1.2-2 Classical Goodness-of-Fit Tests for Univariate Distributions
- gomms-1.0 GLM-Based Ordination Method
- goseq-1.42.0 Gene Ontology analyser for RNA-seq and other length biased data
- gower-0.2.2 Gower’s Distance
- gplots-3.1.1 Various R Programming Tools for Plotting Data
- grDevices built in
- grImport2-0.2-0 Importing ‘SVG’ Graphics
- graph-1.68.0 graph: A package to handle graph data structures
- graphics built in
- graphlayouts-0.7.1 Additional Layout Algorithms for Network Visualizations
- 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-3.3.0 Regularization Paths for Regression Models with Grouped
Covariates
- gsalib-2.1 Utility Functions For GATK
- gsl-2.1-6 Wrapper for the Gnu Scientific Library
- gsubfn-0.7 Utilities for Strings and Function Arguments
- gsw-1.0-5 Gibbs Sea Water Functions
- gtable-0.3.0 Arrange ‘Grobs’ in Tables
- gtools-3.8.2 Various R Programming Tools
- h2o-3.32.0.1 R Interface for the ‘H2O’ Scalable Machine Learning Platform
- hapassoc-1.2-8 Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithm
- haplo.stats-1.8.6 Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
- hardhat-0.1.5 Construct Modeling Packages
- haven-2.3.1 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files
- hdf5r-1.3.3 Interface to the ‘HDF5’ Binary Data Format
- hdm-0.3.1 High-Dimensional Metrics
- hdrcde-3.3 Highest Density Regions and Conditional Density Estimation
- heatmap3-1.1.7 An Improved Heatmap Package
- hexbin-1.28.1 Hexagonal Binning Routines
- hgu133plus2.db-3.2.3 Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2)
- highr-0.8 Syntax Highlighting for R Source Code
- hms-0.5.3 Pretty Time of Day
- hopach-2.50.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
- htmlTable-2.1.0 Advanced Tables for Markdown/HTML
- htmltools-0.5.0 Tools for HTML
- htmlwidgets-1.5.3 HTML Widgets for R
- httpcode-0.3.0 ‘HTTP’ Status Code Helper
- httpuv-1.5.4 HTTP and WebSocket Server Library
- httr-1.4.2 Tools for Working with URLs and HTTP
- huge-1.3.4.1 High-Dimensional Undirected Graph Estimation
- hunspell-3.0.1 High-Performance Stemmer, Tokenizer, and Spell Checker
- hwriter-1.3.2 HTML Writer - Outputs R objects in HTML format
- hypergate-0.8.3 Machine Learning of Hyperrectangular Gating Strategies for
High-Dimensional Cytometry
- ica-1.0-2 Independent Component Analysis
- idr-1.2 Irreproducible discovery rate
- igraph-1.2.6 Network Analysis and Visualization
- igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
- illuminaio-0.32.0 Parsing Illumina Microarray Output Files
- imager-0.42.3 Image Processing Library Based on ‘CImg’
- imagerExtra-1.3.2 Extra Image Processing Library Based on ‘imager’
- impute-1.64.0 impute: Imputation for microarray data
- ineq-0.2-13 Measuring Inequality, Concentration, and Poverty
- infer-0.5.3 Tidy Statistical Inference
- inferference-1.0.0 Methods for Causal Inference with Interference
- influenceR-0.1.0 Software Tools to Quantify Structural Importance of Nodes in a
Network
- infotheo-1.2.0 Information-Theoretic Measures
- ini-0.3.1 Read and Write ‘.ini’ Files
- inline-0.3.17 Functions to Inline C, C++, Fortran Function Calls from R
- interactiveDisplayBase-1.28.0 Base package for enabling powerful shiny web displays of Bioconductor objects
- interpretR-0.2.4 Binary Classifier and Regression Model Interpretation Functions
- inum-1.0-1 Interval and Enum-Type Representation of Vectors
- invgamma-1.1 The Inverse Gamma Distribution
- iotools-0.3-1 I/O Tools for Streaming
- ipred-0.9-9 Improved Predictors
- irace-3.4.1 Iterated Racing for Automatic Algorithm Configuration
- irlba-2.3.3 Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matrices
- isoband-0.2.3 Generate Isolines and Isobands from Regularly Spaced Elevation
Grids
- iterators-1.0.13 Provides Iterator Construct
- itertools-0.1-3 Iterator Tools
- its-1.1.8 Irregular Time Series
- janeaustenr-0.1.5 Jane Austen’s Complete Novels
- jiebaR-0.11 Chinese Text Segmentation
- jiebaRD-0.1 Chinese Text Segmentation Data for jiebaR Package
- jomo-2.7-2 Multilevel Joint Modelling Multiple Imputation
- jpeg-0.1-8.1 Read and write JPEG images
- jsonlite-1.7.2 A Simple and Robust JSON Parser and Generator for R
- karyoploteR-1.16.0 Plot customizable linear genomes displaying arbitrary data
- kedd-1.0.3 Kernel Estimator and Bandwidth Selection for Density and Its
Derivatives
- kernlab-0.9-29 Kernel-Based Machine Learning Lab
- kin.cohort-0.7 Analysis of Kin-Cohort Studies
- kinship2-1.8.5 Pedigree Functions
- klaR-0.6-15 Classification and Visualization
- knitr-1.30 A General-Purpose Package for Dynamic Report Generation in R
- knockoff-0.3.3 The Knockoff Filter for Controlled Variable Selection
- kohonen-3.0.10 Supervised and Unsupervised Self-Organising Maps
- ks-1.11.7 Kernel Smoothing
- kyotil-2020.10-12 Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studies
- labdsv-2.0-1 Ordination and Multivariate Analysis for Ecology
- labeling-0.4.2 Axis Labeling
- labelled-2.7.0 Manipulating Labelled Data
- laeken-0.5.1 Estimation of Indicators on Social Exclusion and Poverty
- lambda.r-1.2.4 Modeling Data with Functional Programming
- lars-1.2 Least Angle Regression, Lasso and Forward Stagewise
- lasso2-1.2-21.1 L1 Constrained Estimation aka `lasso’
- latentnet-2.10.5 Latent Position and Cluster Models for Statistical Networks
- later-1.1.0.1 Utilities for Scheduling Functions to Execute Later with Event
Loops
- lattice-0.20-41 Trellis Graphics for R
- latticeExtra-0.6-29 Extra Graphical Utilities Based on Lattice
- lava-1.6.8.1 Latent Variable Models
- lavaan-0.6-7 Latent Variable Analysis
- lazy-1.2-16 Lazy Learning for Local Regression
- lazyeval-0.2.2 Lazy (Non-Standard) Evaluation
- lda-1.4.2 Collapsed Gibbs Sampling Methods for Topic Models
- leaps-3.1 Regression Subset Selection
- leiden-0.3.6 R Implementation of Leiden Clustering Algorithm
- lhs-1.1.1 Latin Hypercube Samples
- libcoin-1.0-6 Linear Test Statistics for Permutation Inference
- lifecycle-0.2.0 Manage the Life Cycle of your Package Functions
- limSolve-1.5.6 Solving Linear Inverse Models
- limma-3.46.0 Linear Models for Microarray Data
- linprog-0.9-2 Linear Programming / Optimization
- lintr-2.0.1 A ‘Linter’ for R Code
- liquidSVM-1.2.4 A Fast and Versatile SVM Package
- listenv-0.8.0 Environments Behaving (Almost) as Lists
- lme4-1.1-26 Linear Mixed-Effects Models using ‘Eigen’ and S4
- lmerTest-3.1-3 Tests in Linear Mixed Effects Models
- lmtest-0.9-38 Testing Linear Regression Models
- locfdr-1.1-8 Computes Local False Discovery Rates
- locfit-1.5-9.4 Local Regression, Likelihood and Density Estimation
- logcondens-2.1.5 Estimate a Log-Concave Probability Density from Iid Observations
- logistf-1.24 Firth’s Bias-Reduced Logistic Regression
- logspline-2.1.16 Routines for Logspline Density Estimation
- lokern-1.1-8.1 Kernel Regression Smoothing with Local or Global Plug-in
Bandwidth
- longitudinal-1.1.12 Analysis of Multiple Time Course Data
- longmemo-1.1-2 Statistics for Long-Memory Processes (Book Jan Beran), and
Related Functionality
- loo-2.4.1 Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
- lpSolve-5.6.15 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programs
- lpridge-1.0-8 Local Polynomial (Ridge) Regression
- lpsymphony-1.18.0 Symphony integer linear programming solver in R
- lqa-1.0-3 Penalized Likelihood Inference for GLMs
- lsei-1.3-0 Solving Least Squares or Quadratic Programming Problems under
Equality/Inequality Constraints
- lubridate-1.7.9.2 Make Dealing with Dates a Little Easier
- lumi-2.42.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
- mRMRe-2.1.0 “Parallelized Minimum Redundancy, Maximum Relevance (mRMR)
Ensemble Feature Selection”
- maSigPro-1.62.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
- magic-1.5-9 Create and Investigate Magic Squares
- magick-2.5.2 Advanced Graphics and Image-Processing in R
- magrittr-2.0.1 A Forward-Pipe Operator for R
- manipulateWidget-0.10.1 Add Even More Interactivity to Interactive Charts
- mapdata-2.3.0 Extra Map Databases
- mapproj-1.2.7 Map Projections
- maps-3.3.0 Draw Geographical Maps
- maptools-1.0-2 Tools for Handling Spatial Objects
- markdown-1.1 Render Markdown with the C Library ‘Sundown’
- marray-1.68.0 Exploratory analysis for two-color spotted microarray data
- mathjaxr-1.0-1 Using ‘Mathjax’ in Rd Files
- matrixStats-0.57.0 Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
- matrixcalc-1.0-3 Collection of functions for matrix calculations
- maxLik-1.4-6 Maximum Likelihood Estimation and Related Tools
- mboost-2.9-4 Model-Based Boosting
- mclust-5.4.7 Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
- mcmc-0.9-7 Markov Chain Monte Carlo
- medflex-0.6-7 Flexible Mediation Analysis Using Natural Effect Models
- mediation-4.5.0 Causal Mediation Analysis
- memoise-1.1.0 Memoisation of Functions
- memuse-4.1-0 Memory Estimation Utilities
- metagenomeSeq-1.32.0 Statistical analysis for sparse high-throughput sequencing
- methods built in
- methylKit-1.16.0 DNA methylation analysis from high-throughput bisulfite sequencing results
- methylumi-2.36.0 Handle Illumina methylation data
- mets-1.2.8.1 Analysis of Multivariate Event Times
- mgcv-1.8-33 Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
- mi-1.0 Missing Data Imputation and Model Checking
- mice-3.12.0 Multivariate Imputation by Chained Equations
- mime-0.9 Map Filenames to MIME Types
- minfi-1.36.0 Analyze Illumina Infinium DNA methylation arrays
- miniUI-0.1.1.1 Shiny UI Widgets for Small Screens
- minpack.lm-1.2-1 R Interface to the Levenberg-Marquardt Nonlinear Least-Squares
Algorithm Found in MINPACK, Plus Support for Bounds
- minqa-1.2.4 Derivative-free optimization algorithms by quadratic<U+000a>approximation
- misc3d-0.9-0 Miscellaneous 3D Plots
- miscTools-0.6-26 Miscellaneous Tools and Utilities
- missForest-1.4 Nonparametric Missing Value Imputation using Random Forest
- mitml-0.3-7 Tools for Multiple Imputation in Multilevel Modeling
- mitools-2.4 Tools for Multiple Imputation of Missing Data
- mixOmics-6.14.0 Omics Data Integration Project
- mixsqp-0.3-43 Sequential Quadratic Programming for Fast Maximum-Likelihood
Estimation of Mixture Proportions
- mixtools-1.2.0 Tools for Analyzing Finite Mixture Models
- mlbench-2.1-1 Machine Learning Benchmark Problems
- mlegp-3.1.8 Maximum Likelihood Estimates of Gaussian Processes
- mlogit-1.1-1 Multinomial Logit Models
- mlr-2.18.0 Machine Learning in R
- mltools-0.3.5 Machine Learning Tools
- mnormt-2.0.2 The Multivariate Normal and t Distributions, and Their Truncated
Versions
- modeldata-0.1.0 Data Sets Used Useful for Modeling Packages
- modelr-0.1.8 Modelling Functions that Work with the Pipe
- modeltools-0.2-23 Tools and Classes for Statistical Models
- moments-0.14 Moments, cumulants, skewness, kurtosis and related tests
- mondate-0.10.01.02 Keep track of dates in terms of months
- mpath-0.4-2.17 Regularized Linear Models
- msa-1.22.0 Multiple Sequence Alignment
- msigdbr-7.2.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
- msm-1.6.8 Multi-State Markov and Hidden Markov Models in Continuous Time
- multcomp-1.4-15 Simultaneous Inference in General Parametric Models
- multicool-0.1-11 Permutations of Multisets in Cool-Lex Order
- multtest-2.46.0 Resampling-based multiple hypothesis testing
- munsell-0.5.0 Utilities for Using Munsell Colours
- mvabund-4.1.3 Statistical Methods for Analysing Multivariate Abundance Data
- mvnfast-0.2.5.1 Fast Multivariate Normal and Student’s t Methods
- mvtnorm-1.1-1 Multivariate Normal and t Distributions
- nabor-0.5.0 Wraps ‘libnabo’, a Fast K Nearest Neighbour Library for Low
Dimensions
- nanotime-0.3.2 Nanosecond-Resolution Time Support for R
- natserv-1.0.0 ‘NatureServe’ Interface
- ncbit-2013.03.29 retrieve and build NBCI taxonomic data
- ncdf4-1.17 Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
- ncdfFlow-2.36.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
- ndtv-0.13.0 Network Dynamic Temporal Visualizations
- network-1.16.1 Classes for Relational Data
- networkDynamic-0.10.1 Dynamic Extensions for Network Objects
- networksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through
Sequential Importance Sampling
- neuRosim-0.2-12 Functions to Generate fMRI Data Including Activated Data, Noise
Data and Resting State Data
- nleqslv-3.3.2 Solve Systems of Nonlinear Equations
- nlme-3.1-151 Linear and Nonlinear Mixed Effects Models
- nloptr-1.2.2.2 R Interface to NLopt
- nnet-7.3-14 Feed-Forward Neural Networks and Multinomial Log-Linear Models
- nnls-1.4 The Lawson-Hanson algorithm for non-negative least squares<U+000a>(NNLS)
- nor1mix-1.3-0 Normal aka Gaussian (1-d) Mixture Models (S3 Classes and
Methods)
- np-0.60-10 Nonparametric Kernel Smoothing Methods for Mixed Data Types
- npsurv-0.5-0 Nonparametric Survival Analysis
- numDeriv-2016.8-1.1 Accurate Numerical Derivatives
- numbers-0.7-5 Number-Theoretic Functions
- nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
- oce-1.2-0 Analysis of Oceanographic Data
- oddsratio-2.0.1 Odds Ratio Calculation for GAM(M)s & GLM(M)s
- oligoClasses-1.52.0 Classes for high-throughput arrays supported by oligo and crlmm
- openCyto-2.2.0 Hierarchical Gating Pipeline for flow cytometry data
- openssl-1.4.3 Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
- openxlsx-4.2.3 Read, Write and Edit xlsx Files
- operator.tools-1.6.3 Utilities for Working with R’s Operators
- optmatch-0.9-13 Functions for Optimal Matching
- optparse-1.6.6 Command Line Option Parser
- ordinal-2019.12-10 Regression Models for Ordinal Data
- org.Hs.eg.db-3.12.0 Genome wide annotation for Human
- org.Mm.eg.db-3.12.0 Genome wide annotation for Mouse
- oro.nifti-0.11.0 Rigorous - ‘NIfTI’ + ‘ANALYZE’ + ‘AFNI’ : Input / Output
- pROC-1.16.2 Display and Analyze ROC Curves
- pack-0.1-1 Convert values to/from raw vectors
- packrat-0.5.0 A Dependency Management System for Projects and their R Package
Dependencies
- pamr-1.56.1 Pam: Prediction Analysis for Microarrays
- pan-1.6 Multiple Imputation for Multivariate Panel or Clustered Data
- parallelMap-1.5.0 Unified Interface to Parallelization Back-Ends
- parallelly-1.22.0 Enhancing the ‘parallel’ Package
- parsedate-1.2.0 Recognize and Parse Dates in Various Formats, Including All ISO
8601 Formats
- parsnip-0.1.4 A Common API to Modeling and Analysis Functions
- partools-1.1.6 Tools for the ‘Parallel’ Package
- party-1.3-5 A Laboratory for Recursive Partytioning
- partykit-1.2-11 A Toolkit for Recursive Partytioning
- pastecs-1.3.21 Package for Analysis of Space-Time Ecological Series
- patchwork-1.1.1 The Composer of Plots
- pathview-1.30.1 a tool set for pathway based data integration and visualization
- pbapply-1.4-3 Adding Progress Bar to ‘*apply’ Functions
- pbivnorm-0.6.0 Vectorized Bivariate Normal CDF
- pbkrtest-0.4-8.6 Parametric Bootstrap, Kenward-Roger and Satterthwaite Based
Methods for Test in Mixed Models
- pbs-1.1 Periodic B Splines
- pcaMethods-1.82.0 A collection of PCA methods
- pcaPP-1.9-73 Robust PCA by Projection Pursuit
- pdftools-2.3.1 Text Extraction, Rendering and Converting of PDF Documents
- pdist-1.2 Partitioned Distance Function
- pedigree-1.4 Pedigree functions
- pedigreemm-0.3-3 Pedigree-based mixed-effects models
- penalized-0.9-51 L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
in GLMs and in the Cox Model
- peperr-1.1-7.1 Parallelised Estimation of Prediction Error
- perm-1.0-0.0 Exact or Asymptotic permutation tests
- permute-0.9-5 Functions for Generating Restricted Permutations of Data
- phangorn-2.5.5 Phylogenetic Reconstruction and Analysis
- pheatmap-1.0.12 Pretty Heatmaps
- phylobase-0.8.10 Base Package for Phylogenetic Structures and Comparative Data
- phyloseq-1.34.0 Handling and analysis of high-throughput microbiome census data
- phytools-0.7-70 Phylogenetic Tools for Comparative Biology (and Other Things)
- pillar-1.4.7 Coloured Formatting for Columns
- pim-2.0.2 Fit Probabilistic Index Models
- pinfsc50-1.2.0 Sequence (‘FASTA’), Annotation (‘GFF’) and Variants (‘VCF’) for
17 Samples of ‘P. Infestans” and 1 ‘P. Mirabilis’
- pixmap-0.4-11 Bitmap Images (``Pixel Maps’’)
- pkgbuild-1.2.0 Find Tools Needed to Build R Packages
- pkgconfig-2.0.3 Private Configuration for ‘R’ Packages
- pkgload-1.1.0 Simulate Package Installation and Attach
- pkgmaker-0.32.2 Development Utilities for R Packages
- plogr-0.2.0 The ‘plog’ C++ Logging Library
- plot3D-1.3 Plotting Multi-Dimensional Data
- plot3Drgl-1.0.1 Plotting Multi-Dimensional Data - Using ‘rgl’
- plotly-4.9.2.1 Create Interactive Web Graphics via ‘plotly.js’
- plotrix-3.7-8 Various Plotting Functions
- pls-2.7-3 Partial Least Squares and Principal Component Regression
- plyr-1.8.6 Tools for Splitting, Applying and Combining Data
- png-0.1-7 Read and write PNG images
- poisbinom-1.0.1 A Faster Implementation of the Poisson-Binomial Distribution
- polspline-1.1.19 Polynomial Spline Routines
- polyclip-1.10-0 Polygon Clipping
- polyester-1.26.0 Simulate RNA-seq reads
- polynom-1.4-0 A Collection of Functions to Implement a Class for Univariate
Polynomial Manipulations
- poweRlaw-0.70.6 Analysis of Heavy Tailed Distributions
- prabclus-2.3-2 Functions for Clustering and Testing of Presence-Absence,
Abundance and Multilocus Genetic Data
- pracma-2.2.9 Practical Numerical Math Functions
- praise-1.0.0 Praise Users
- preprocessCore-1.52.0 A collection of pre-processing functions
- preseqR-4.0.0 Predicting Species Accumulation Curves
- presto 1.0.0
- prettyunits-1.1.1 Pretty, Human Readable Formatting of Quantities
- processx-3.4.5 Execute and Control System Processes
- prodlim-2019.11.13 Product-Limit Estimation for Censored Event History Analysis
- profileModel-0.6.0 Profiling Inference Functions for Various Model Classes
- progress-1.2.2 Terminal Progress Bars
- promises-1.1.1 Abstractions for Promise-Based Asynchronous Programming
- proto-1.0.0 Prototype Object-Based Programming
- proxy-0.4-24 Distance and Similarity Measures
- pryr-0.1.4 Tools for Computing on the Language
- ps-1.5.0 List, Query, Manipulate System Processes
- pscl-1.5.5 Political Science Computational Laboratory
- pspline-1.0-18 Penalized Smoothing Splines
- psych-2.0.12 Procedures for Psychological, Psychometric, and Personality
Research
- psychotools-0.6-0 Psychometric Modeling Infrastructure
- pulsar-0.3.7 Parallel Utilities for Lambda Selection along a Regularization
Path
- purrr-0.3.4 Functional Programming Tools
- pvclust-2.2-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap
Resampling
- qdapRegex-0.7.2 Regular Expression Removal, Extraction, and Replacement Tools
- qgam-1.3.2 Smooth Additive Quantile Regression Models
- qgraph-1.6.5 Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
- qpdf-1.1 Split, Combine and Compress PDF Files
- qrnn-2.0.5 Quantile Regression Neural Network
- qtl-1.46-2 Tools for Analyzing QTL Experiments
- quadprog-1.5-8 Functions to Solve Quadratic Programming Problems
- quantmod-0.4.18 Quantitative Financial Modelling Framework
- quantreg-5.75 Quantile Regression
- quantsmooth-1.56.0 Quantile smoothing and genomic visualization of array data
- questionr-0.7.4 Functions to Make Surveys Processing Easier
- qvalue-2.22.0 Q-value estimation for false discovery rate control
- qvcalc-1.0.2 Quasi Variances for Factor Effects in Statistical Models
- r2d3-0.2.5 Interface to ‘D3’ Visualizations
- rARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD Problems
- rGADEM-2.38.0 de novo motif discovery
- rJava-0.9-13 Low-Level R to Java Interface
- rainbow-3.6 Bagplots, Boxplots and Rainbow Plots for Functional Data
- randomForest-4.6-14 Breiman and Cutler’s Random Forests for Classification and
Regression
- randomForestSRC-2.9.3 Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
- ranger-0.12.1 A Fast Implementation of Random Forests
- rappdirs-0.3.1 Application Directories: Determine Where to Save Data, Caches,
and Logs
- raster-3.4-5 Geographic Data Analysis and Modeling
- rasterVis-0.49 Visualization Methods for Raster Data
- rbenchmark-1.0.0 Benchmarking routine for R
- rbibutils-2.0 Convert Between Bibliography Formats
- rcmdcheck-1.3.3 Run ‘R CMD check’ from ‘R’ and Capture Results
- rda-1.0.2-2.1 Shrunken Centroids Regularized Discriminant Analysis
- readbitmap-0.1.5 Simple Unified Interface to Read Bitmap Images
(BMP,JPEG,PNG,TIFF)
- readr-1.4.0 Read Rectangular Text Data
- readxl-1.3.1 Read Excel Files
- recipes-0.1.15 Preprocessing Tools to Create Design Matrices
- refGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from
‘Ensembl’ and ‘UCSC’ Genome Browsers
- refund-0.1-23 Regression with Functional Data
- regioneR-1.22.0 Association analysis of genomic regions based on permutation tests
- registry-0.5-1 Infrastructure for R Package Registries
- regress-1.3-21 Gaussian Linear Models with Linear Covariance Structure
- regtools-1.1.0 Regression and Classification Tools
- relations-0.6-9 Data Structures and Algorithms for Relations
- relevent-1.0-4 Relational Event Models
- rematch-1.0.1 Match Regular Expressions with a Nicer ‘API’
- rematch2-2.1.2 Tidy Output from Regular Expression Matching
- remotes-2.2.0 R Package Installation from Remote Repositories, Including
‘GitHub’
- rentrez-1.2.3 ‘Entrez’ in R
- repr-1.1.0 Serializable Representations
- reprex-0.3.0 Prepare Reproducible Example Code via the Clipboard
- resample-0.4 Resampling Functions
- reshape-0.8.8 Flexibly Reshape Data
- reshape2-1.4.4 Flexibly Reshape Data: A Reboot of the Reshape Package
- reticulate-1.18 Interface to ‘Python’
- rex-1.2.0 Friendly Regular Expressions
- rgenoud-5.8-3.0 R Version of GENetic Optimization Using Derivatives
- rgexf-0.16.0 Build, Import and Export GEXF Graph Files
- rgl-0.103.5 3D Visualization Using OpenGL
- rhdf5-2.34.0 R Interface to HDF5
- rhdf5filters-1.2.0 HDF5 Compression Filters
- rio-0.5.16 A Swiss-Army Knife for Data I/O
- ritis-0.9.0 Integrated Taxonomic Information System Client
- rjags-4-10 Bayesian Graphical Models using MCMC
- rjson-0.2.20 JSON for R
- rlang-0.4.9 Functions for Base Types and Core R and ‘Tidyverse’ Features
- rle-0.9.2 Common Functions for Run-Length Encoded Vectors
- rlecuyer-0.3-5 R Interface to RNG with Multiple Streams
- rmarkdown-2.6 Dynamic Documents for R
- rmeta-3.0 Meta-Analysis
- rms-6.1-0 Regression Modeling Strategies
- rncl-0.8.4 An Interface to the Nexus Class Library
- rngtools-1.5 Utility Functions for Working with Random Number Generators
- robustbase-0.93-6 Basic Robust Statistics
- rootSolve-1.8.2.1 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of
Ordinary Differential Equations
- rotl-3.0.11 Interface to the ‘Open Tree of Life’ API
- roxygen2-7.1.1 In-Line Documentation for R
- rpart-4.1-15 Recursive Partitioning and Regression Trees
- rprojroot-2.0.2 Finding Files in Project Subdirectories
- rrcov-1.5-5 Scalable Robust Estimators with High Breakdown Point
- rredlist-0.7.0 ‘IUCN’ Red List Client
- rsample-0.0.8 General Resampling Infrastructure
- rsconnect-0.8.16 Deployment Interface for R Markdown Documents and Shiny
Applications
- rslurm-0.5.0 Submit R Calculations to a ‘Slurm’ Cluster
- rstan-2.21.2 R Interface to Stan
- rstanarm-2.21.1 Bayesian Applied Regression Modeling via Stan
- rstantools-2.1.1 Tools for Developing R Packages Interfacing with ‘Stan’
- rstatix-0.6.0 Pipe-Friendly Framework for Basic Statistical Tests
- rstudioapi-0.13 Safely Access the RStudio API
- rsvd-1.0.3 Randomized Singular Value Decomposition
- rsvg-2.1 Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
- rtracklayer-1.50.0 R interface to genome annotation files and the UCSC genome browser
- rvcheck-0.1.8 R/Package Version Check
- rversions-2.0.2 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
- rvest-0.3.6 Easily Harvest (Scrape) Web Pages
- rzmq-0.9.7 R Bindings for ‘ZeroMQ’
- sampling-2.8 Survey Sampling
- samr-3.0 SAM: Significance Analysis of Microarrays
- sandwich-3.0-0 Robust Covariance Matrix Estimators
- scales-1.1.1 Scale Functions for Visualization
- scattermore-0.7 Scatterplots with More Points
- scatterpie-0.1.5 Scatter Pie Plot
- scatterplot3d-0.3-41 3D Scatter Plot
- schoolmath-0.4 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
- sctransform-0.3.2 Variance Stabilizing Transformations for Single Cell UMI Data
- seewave-2.1.6 Sound Analysis and Synthesis
- segmented-1.3-1 Regression Models with Break-Points / Change-Points Estimation
- selectr-0.4-2 Translate CSS Selectors to XPath Expressions
- sem-3.1-11 Structural Equation Models
- sendmailR-1.2-1 send email using R
- seqLogo-1.56.0 Sequence logos for DNA sequence alignments
- seqinr-4.2-4 Biological Sequences Retrieval and Analysis
- seqminer-8.0 Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into R
- sequenza-3.0.0 Copy Number Estimation from Tumor Genome Sequencing Data
- servr-0.21 A Simple HTTP Server to Serve Static Files or Dynamic Documents
- sessioninfo-1.1.1 R Session Information
- sets-1.0-18 Sets, Generalized Sets, Customizable Sets and Intervals
- sfsmisc-1.1-7 Utilities from ‘Seminar fuer Statistik’ ETH Zurich
- shadowtext-0.0.7 Shadow Text Grob and Layer
- shape-1.4.5 Functions for Plotting Graphical Shapes, Colors
- shapefiles-0.7 Read and Write ESRI Shapefiles
- shiny-1.5.0 Web Application Framework for R
- shinyBS-0.61 Twitter Bootstrap Components for Shiny
- shinyFiles-0.9.0 A Server-Side File System Viewer for Shiny
- shinycssloaders-1.0.0 Add Loading Animations to a ‘shiny’ Output While It’s
Recalculating
- shinydashboard-0.7.1 Create Dashboards with ‘Shiny’
- shinyjs-2.0.0 Easily Improve the User Experience of Your Shiny Apps in Seconds
- shinystan-2.5.0 Interactive Visual and Numerical Diagnostics and Posterior
Analysis for Bayesian Models
- shinythemes-1.1.2 Themes for Shiny
- sigaR-1.35.0 Statistics for Integrative Genomics Analyses in R
- siggenes-1.64.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
- signal-0.7-6 Signal Processing
- sitmo-2.0.1 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header
Files
- slam-0.1-48 Sparse Lightweight Arrays and Matrices
- slider-0.1.5 Sliding Window Functions
- sm-2.2-5.6 Smoothing Methods for Nonparametric Regression and Density
Estimation
- smfishHmrf-0.1 Hidden Markov Random Field for Spatial Transcriptomic Data
- smoother-1.1 Functions Relating to the Smoothing of Numerical Data
- sn-1.6-2 The Skew-Normal and Related Distributions Such as the Skew-t
- sna-2.6 Tools for Social Network Analysis
- snow-0.4-3 Simple Network of Workstations
- snowfall-1.84-6.1 Easier cluster computing (based on snow).
- snpStats-1.40.0 SnpMatrix and XSnpMatrix classes and methods
- solrium-1.1.4 General Purpose R Interface to ‘Solr’
- som-0.3-5.1 Self-Organizing Map
- soundecology-1.3.3 Soundscape Ecology
- sourcetools-0.1.7 Tools for Reading, Tokenizing and Parsing R Code
- sp-1.4-4 Classes and Methods for Spatial Data
- spData-0.3.8 Datasets for Spatial Analysis
- spaMM-3.5.0 Mixed-Effect Models, Particularly Spatial Models
- spam-2.6-0 SPArse Matrix
- sparklyr-1.5.2 R Interface to Apache Spark
- sparseMatrixStats-1.2.0 Summary Statistics for Rows and Columns of Sparse Matrices
- spatial-7.3-12 Functions for Kriging and Point Pattern Analysis
- spatstat-1.64-1 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
- spatstat.data-1.7-0 Datasets for ‘spatstat’
- spatstat.utils-1.17-0 Utility Functions for ‘spatstat’
- 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
- sqldf-0.4-11 Manipulate R Data Frames Using SQL
- squash-1.0.9 Color-Based Plots for Multivariate Visualization
- ssgraph-1.12 Bayesian Graphical Estimation using Spike-and-Slab Priors
- stabledist-0.7-1 Stable Distribution Functions
- stabs-0.6-3 Stability Selection with Error Control
- startupmsg-0.9.6 Utilities for Start-Up Messages
- statmod-1.4.35 Statistical Modeling
- statnet-2019.6 Software Tools for the Statistical Analysis of Network Data
- statnet.common-4.4.1 Common R Scripts and Utilities Used by the Statnet Project
Software
- stats built in
- stats4 built in
- stopwords-2.1 Multilingual Stopword Lists
- stringdist-0.9.6.3 Approximate String Matching, Fuzzy Text Search, and String
Distance Functions
- stringi-1.5.3 Character String Processing Facilities
- stringr-1.4.0 Simple, Consistent Wrappers for Common String Operations
- strucchange-1.5-2 Testing, Monitoring, and Dating Structural Changes
- styler-1.3.2 Non-Invasive Pretty Printing of R Code
- subplex-1.6 Unconstrained Optimization using the Subplex Algorithm
- survey-4.0 Analysis of Complex Survey Samples
- survival-3.2-7 Survival Analysis
- survivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival data
- sva-3.38.0 Surrogate Variable Analysis
- svd-0.5 Interfaces to Various State-of-Art SVD and Eigensolvers
- sys-3.4 Powerful and Reliable Tools for Running System Commands in R
- systemPipeR-1.24.2 systemPipeR: NGS workflow and report generation environment
- systemfonts-0.3.2 System Native Font Finding
- tables-0.9.6 Formula-Driven Table Generation
- taxize-0.9.99 Taxonomic Information from Around the Web
- tclust-1.4-2 Robust Trimmed Clustering
- tensor-1.5 Tensor product of arrays
- tensorA-0.36.2 Advanced Tensor Arithmetic with Named Indices
- tergm-3.7.0 Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
- tergmLite-2.2.1 Fast Simulation of Simple Temporal Exponential Random Graph
Models
- testthat-3.0.0 Unit Testing for R
- threejs-0.3.3 Interactive 3D Scatter Plots, Networks and Globes
- tibble-3.0.4 Simple Data Frames
- tictoc-1.0 Functions for timing R scripts, as well as implementations of
Stack and List structures.
- tidygraph-1.2.0 A Tidy API for Graph Manipulation
- tidymodels-0.1.2 Easily Install and Load the ‘Tidymodels’ Packages
- tidyposterior-0.0.3 Bayesian Analysis to Compare Models using Resampling Statistics
- tidypredict-0.4.8 Run Predictions Inside the Database
- tidyr-1.1.2 Tidy Messy Data
- tidyselect-1.1.0 Select from a Set of Strings
- tidytext-0.2.6 Text Mining using ‘dplyr’, ‘ggplot2’, and Other Tidy Tools
- tidytree-0.3.3 A Tidy Tool for Phylogenetic Tree Data Manipulation
- tidyverse-1.3.0 Easily Install and Load the ‘Tidyverse’
- tiff-0.1-6 Read and write TIFF images
- tilingArray-1.68.0 Transcript mapping with high-density oligonucleotide tiling arrays
- timeDate-3043.102 Rmetrics - Chronological and Calendar Objects
- timeSeries-3062.100 Financial Time Series Objects (Rmetrics)
- timereg-1.9.8 Flexible Regression Models for Survival Data
- tinytex-0.28 Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
- tkWidgets-1.68.0 R based tk widgets
- tkrplot-0.0-24 TK Rplot
- tm-0.7-8 Text Mining Package
- tmle-1.5.0-1 Targeted Maximum Likelihood Estimation
- tmvnsim-1.0-2 Truncated Multivariate Normal Simulation
- tmvtnorm-1.4-10 Truncated Multivariate Normal and Student t Distribution
- tokenizers-0.2.1 Fast, Consistent Tokenization of Natural Language Text
- tools built in
- topicmodels-0.2-11 Topic Models
- tree-1.0-40 Classification and Regression Trees
- treeio-1.14.3 Base Classes and Functions for Phylogenetic Tree Input and Output
- triebeard-0.3.0 ‘Radix’ Trees in ‘Rcpp’
- trimcluster-0.1-5 Cluster Analysis with Trimming
- tripack-1.3-9.1 Triangulation of Irregularly Spaced Data
- truncnorm-1.0-8 Truncated Normal Distribution
- trust-0.1-8 Trust Region Optimization
- tseries-0.10-48 Time Series Analysis and Computational Finance
- tseriesChaos-0.1-13.1 Analysis of Nonlinear Time Series
- tsna-0.3.1 Tools for Temporal Social Network Analysis
- tsne-0.1-3 T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
- tune-0.1.2 Tidy Tuning Tools
- tuneR-1.3.3 Analysis of Music and Speech
- tweedie-2.3.2 Evaluation of Tweedie Exponential Family Models
- tweenr-1.0.1 Interpolate Data for Smooth Animations
- ucminf-1.1-4 General-Purpose Unconstrained Non-Linear Optimization
- udunits2-0.13 Udunits-2 Bindings for R
- unbalanced-2.0 Racing for Unbalanced Methods Selection
- uniqueAtomMat-0.1-3-2 Finding Unique or Duplicated Rows or Columns for Atomic Matrices
- units-0.6-7 Measurement Units for R Vectors
- urca-1.3-0 Unit Root and Cointegration Tests for Time Series Data
- urltools-1.7.3 Vectorised Tools for URL Handling and Parsing
- uroot-2.1-2 Unit Root Tests for Seasonal Time Series
- usethis-2.0.0 Automate Package and Project Setup
- utf8-1.1.4 Unicode Text Processing
- utils built in
- uuid-0.1-4 Tools for Generating and Handling of UUIDs
- uwot-0.1.10 The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
- vcd-1.4-8 Visualizing Categorical Data
- vcfR-1.12.0 Manipulate and Visualize VCF Data
- vctrs-0.3.5 Vector Helpers
- vegan-2.5-7 Community Ecology Package
- venn-1.9 Draw Venn Diagrams
- vimp-2.1.0 Perform Inference on Algorithm-Agnostic Variable Importance
- vioplot-0.3.5 Violin Plot
- vipor-0.4.5 Plot Categorical Data Using Quasirandom Noise and Density
Estimates
- viridis-0.5.1 Default Color Maps from ‘matplotlib’
- viridisLite-0.3.0 Default Color Maps from ‘matplotlib’ (Lite Version)
- visNetwork-2.0.9 Network Visualization using ‘vis.js’ Library
- vsn-3.58.0 Variance stabilization and calibration for microarray data
- waldo-0.2.3 Find Differences Between R Objects
- warp-0.2.0 Group Dates
- waveslim-1.8.2 Basic Wavelet Routines for One-, Two-, and Three-Dimensional
Signal Processing
- wavethresh-4.6.8 Wavelets Statistics and Transforms
- webp-1.0 A New Format for Lossless and Lossy Image Compression
- webshot-0.5.2 Take Screenshots of Web Pages
- whisker-0.4 for R, Logicless Templating
- widgetTools-1.68.0 Creates an interactive tcltk widget
- wikitaxa-0.4.0 Taxonomic Information from ‘Wikipedia’
- withr-2.3.0 Run Code ‘With’ Temporarily Modified Global State
- workflows-0.2.1 Modeling Workflows
- worrms-0.4.2 World Register of Marine Species (WoRMS) Client
- xCell 1.1.0
- xfun-0.19 Miscellaneous Functions by ‘Yihui Xie’
- xgboost-1.2.0.1 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
- xml2-1.3.2 Parse XML
- xmlparsedata-1.0.4 Parse Data of ‘R’ Code as an ‘XML’ Tree
- xopen-1.0.0 Open System Files, ‘URLs’, Anything
- xtable-1.8-4 Export Tables to LaTeX or HTML
- xts-0.12.1 eXtensible Time Series
- yaml-2.2.1 Methods to Convert R Data to YAML and Back
- yardstick-0.0.7 Tidy Characterizations of Model Performance
- zCompositions-1.3.4 Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Sets
- zeallot-0.1.0 Multiple, Unpacking, and Destructuring Assignment
- zip-2.1.1 Cross-Platform ‘zip’ Compression
- zlibbioc-1.36.0 An R packaged zlib-1.2.5
- zoo-1.8-8 S3 Infrastructure for Regular and Irregular Time Series (Z’s
Ordered Observations)