fhR-4.1.2-foss-2021b

Known Issues

• None

Package List

• ADGofTest-0.3 Anderson-Darling GoF test
• AICcmodavg-2.3-1 Model Selection and Multimodel Inference Based on (Q)AIC(c)
• ALDEx2-1.26.0 Analysis Of Differential Abundance Taking Sample Variation Into Account
• ALL-1.36.0 A data package
• ASCAT 2.5.2
• AUC-0.3.0 Threshold Independent Performance Measures for Probabilistic Classifiers
• AgiMicroRna-2.44.0 Processing and Differential Expression Analysis of Agilent microRNA chips
• AlgDesign-1.2.0 Algorithmic Experimental Design
• AnalyzeFMRI-1.1-24 Functions for Analysis of fMRI Datasets Stored in the ANALYZE or NIFTI Format
• AnnotationDbi-1.56.2 Manipulation of SQLite-based annotations in Bioconductor
• AnnotationFilter-1.18.0 Facilities for Filtering Bioconductor Annotation Resources
• AnnotationForge-1.36.0 Tools for building SQLite-based annotation data packages
• AnnotationHub-3.2.0 Client to access AnnotationHub resources
• ArchR 1.0.1
• 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-2.64 Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
• BH-1.75.0-0 Boost C++ Header Files
• BIGL-1.6.5 Biochemically Intuitive Generalized Loewe Model
• BMA-3.18.15 Bayesian Model Averaging
• BSgenome-1.62.0 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-2.54.0 Biobase: Base functions for Bioconductor
• BiocFileCache-2.2.0 Manage Files Across Sessions
• BiocGenerics-0.40.0 S4 generic functions used in Bioconductor
• BiocIO-1.4.0 Standard Input and Output for Bioconductor Packages
• BiocManager-1.30.16 Access the Bioconductor Project Package Repository
• BiocNeighbors-1.12.0 Nearest Neighbor Detection for Bioconductor Packages
• BiocParallel-1.28.1 Bioconductor facilities for parallel evaluation
• BiocSingular-1.10.0 Singular Value Decomposition for Bioconductor Packages
• BiocStyle-2.22.0 Standard styles for vignettes and other Bioconductor documents
• BiocVersion-3.14.0 Set the appropriate version of Bioconductor packages
• Biostrings-2.62.0 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
• CATALYST-1.18.0 Cytometry dATa anALYSis Tools
• CBPS-0.22 Covariate Balancing Propensity Score
• CGHbase-1.54.0 CGHbase: Base functions and classes for arrayCGH data analysis.
• CLONETv2-2.2.1 Clonality Estimates in Tumor
• CMA-1.52.0 Synthesis of microarray-based classification
• CNEr-1.30.0 CNE Detection and Visualization
• COMPASS-1.32.0 Combinatorial Polyfunctionality Analysis of Single Cells
• CVST-0.2-2 Fast Cross-Validation via Sequential Testing
• CVXR-1.0-10 Disciplined Convex Optimization
• 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-2.60.0 Category Analysis
• ChIPpeakAnno-3.28.0 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
• ChIPseeker-1.30.2 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-2.10.0 Make Complex Heatmaps
• ConsensusClusterPlus-1.58.0 ConsensusClusterPlus
• CovSel-1.2.1 Model-Free Covariate Selection
• CytoML-2.6.0 A GatingML Interface for Cross Platform Cytometry Data Sharing
• DAAG-1.24 Data Analysis and Graphics Data and Functions
• DBI-1.1.1 R Database Interface
• DECIPHER-2.22.0 Tools for curating, analyzing, and manipulating biological sequences
• DEGseq-1.48.0 Identify Differentially Expressed Genes from RNA-seq data
• DESeq2-1.34.0 Differential gene expression analysis based on the negative binomial distribution
• DEoptim-2.2-6 Global Optimization by Differential Evolution
• DEoptimR-1.0-9 Differential Evolution Optimization in Pure R
• DHARMa-0.4.4 Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
• DMCfun-2.0.2 Diffusion Model of Conflict (DMC) in Reaction Time Tasks
• DNAcopy-1.68.0 DNA copy number data analysis
• DO.db-2.9 A set of annotation maps describing the entire Disease Ontology
• DOSE-3.20.1 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-0.19 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-0.20.0 A unified framework for working transparently with on-disk and in-memory array-like datasets
• DelayedMatrixStats-1.16.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
• Deriv-4.1.3 Symbolic Differentiation
• DescTools-0.99.43 Tools for Descriptive Statistics
• DiagrammeR-1.0.6.1 Graph/Network Visualization
• DiceDesign-1.9 Designs of Computer Experiments
• DiceKriging-1.6.0 Kriging Methods for Computer Experiments
• DiffBind-3.4.0 Differential Binding Analysis of ChIP-Seq Peak Data
• DirichletMultinomial-1.36.0 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-1.72.0 Dynamic document tools
• EBImage-4.36.0 Image processing and analysis toolbox for R
• ECOSolveR-0.5.4 Embedded Conic Solver in R
• ENMeval-2.0.1 Automated Tuning and Evaluations of Ecological Niche Models
• EasyABC-1.5 Efficient Approximate Bayesian Computation Sampling Schemes
• EnvStats-2.4.0 Package for Environmental Statistics, Including US EPA Guidance
• EpiModel-2.2.0 Mathematical Modeling of Infectious Disease Dynamics
• Exact-3.0 Unconditional Exact Test
• FDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probes
• FME-1.3.6.2 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-2.2.0 Using self-organizing maps for visualization and interpretation of cytometry data
• Formula-1.2-4 Extended Model Formulas
• GENESIS-2.24.0 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
• GEOquery-2.62.1 Get data from NCBI Gene Expression Omnibus (GEO)
• GGally-2.1.2 Extension to ‘ggplot2’
• GO.db-3.14.0 A set of annotation maps describing the entire Gene Ontology
• GOSemSim-2.20.0 GO-terms Semantic Similarity Measures
• GOstats-2.60.0 Tools for manipulating GO and microarrays
• GPfit-1.0-8 Gaussian Processes Modeling
• GSA-1.03.1 Gene Set Analysis
• GSEABase-1.56.0 Gene set enrichment data structures and methods
• GSVA-1.42.0 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-1.40.0 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-1.30.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
• GenomeInfoDbData-1.2.7 Species and taxonomy ID look up tables used by GenomeInfoDb
• GenomicAlignments-1.30.0 Representation and manipulation of short genomic alignments
• GenomicFeatures-1.46.1 Conveniently import and query gene models
• GenomicFiles-1.30.0 Distributed computing by file or by range
• GenomicRanges-1.46.1 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-2.4.0 Interactive HTML graphics
• GlobalOptions-0.1.2 Generate Functions to Get or Set Global Options
• Gmisc-2.1.0 Descriptive Statistics, Transition Plots, and More
• GreyListChIP-1.26.0 Grey Lists – Mask Artefact Regions Based on ChIP Inputs
• Gviz-1.38.0 Plotting data and annotation information along genomic coordinates
• GxEScanR-2.0.2 Run GWAS/GWEIS Scans Using Binary Dosage Files
• HDF5Array-1.22.1 HDF5 backend for DelayedArray objects
• HMMcopy-1.36.0 Copy number prediction with correction for GC and mappability bias for HTS data
• HSMMSingleCell-1.14.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)
• HWxtest-1.1.9 Exact Tests for Hardy-Weinberg Proportions
• HaploSim-1.8.4 Functions to simulate haplotypes
• HiddenMarkov-1.8-13 Hidden Markov Models
• Hmisc-4.6-0 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)’
• IHW-1.22.0 Independent Hypothesis Weighting
• IRanges-2.28.0 Foundation of integer range manipulation in Bioconductor
• IRdisplay-1.0 ‘Jupyter’ Display Machinery
• ISOcodes-2021.02.24 Selected ISO Codes
• IlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arrays
• InteractionSet-1.22.0 Base Classes for Storing Genomic Interaction Data
• Iso-0.0-18.1 Functions to Perform Isotonic Regression
• JADE-2.0-3 Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria
• JBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J. Buttlar
• KEGGREST-1.34.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
• KEGGgraph-1.54.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
• KODAMA-1.8 Knowledge Discovery by Accuracy Maximization
• KernSmooth-2.23-20 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
• 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
• LogicReg-1.6.4 Logic Regression
• LymphoSeq-1.22.0 Analyze high-throughput sequencing of T and B cell receptors
• LymphoSeqDB-0.99.2 LymphoSeq annotation databases
• MAGeCKFlute-1.14.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
• MALDIquant-1.20 Quantitative Analysis of Mass Spectrometry Data
• MASS-7.3-54 Support Functions and Datasets for Venables and Ripley’s MASS
• MAST-1.20.0 Model-based Analysis of Single Cell Transcriptomics
• MCMCglmm-2.32 MCMC Generalised Linear Mixed Models
• MCMCpack-1.6-0 Markov Chain Monte Carlo (MCMC) Package
• MIIVsem-0.5.8 Model Implied Instrumental Variable (MIIV) Estimation of Structural Equation Models
• MPV-1.57 Data Sets from Montgomery, Peck and Vining
• MatchIt-4.3.0 Nonparametric Preprocessing for Parametric Causal Inference
• Matching-4.9-11 Multivariate and Propensity Score Matching with Balance Optimization
• Matrix-1.3-4 Sparse and Dense Matrix Classes and Methods
• MatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations
• MatrixGenerics-1.6.0 S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
• MatrixModels-0.5-0 Modelling with Sparse and Dense Matrices
• Mfuzz-2.54.0 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
• NCmisc-1.1.6 Miscellaneous Functions for Creating Adaptive Functions and Scripts
• NISTunits-1.0.1 Fundamental Physical Constants and Unit Conversions from NIST
• NLP-0.2-1 Natural Language Processing Infrastructure
• NOISeq-2.38.0 Exploratory analysis and differential expression for RNA-seq data
• OceanView-1.0.6 Visualisation of Oceanographic Data and Model Output
• OrganismDbi-1.36.0 Software to enable the smooth interfacing of different database packages
• PBSddesolve-1.12.6 Solver for Delay Differential Equations
• PCAmatchR-0.3.0 Match Cases to Controls Based on Genotype Principal Components
• PFAM.db-3.14.0 A set of protein ID mappings for PFAM
• PICS-2.38.0 Probabilistic inference of ChIP-seq
• ParamHelpers-1.14 Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning
• PermAlgo-1.1 Permutational Algorithm to Simulate Survival Data
• 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-1.26.0 Generic infrastructure for Bioconductor mass spectrometry packages
• QUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix Estimation
• R.cache-0.15.0 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-2.11.0 Various Programming Utilities
• R2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
• R2jags-0.7-1 Using R to Run ‘JAGS’
• R6-2.5.1 Encapsulated Classes with Reference Semantics
• RANN-2.6.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric
• RBGL-1.70.0 An interface to the BOOST graph library
• RCAL-2.0 Regularized Calibrated Estimation
• RCircos-1.2.1 Circos 2D Track Plot
• RColorBrewer-1.1-2 ColorBrewer Palettes
• RCurl-1.98-1.5 General Network (HTTP/FTP/…) Client Interface for R
• REDCapR-1.0.0 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-1.3-1.6 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 Theory
• RNASeqPower-1.34.0 Sample size for RNAseq studies
• RNeXML-2.4.5 Semantically Rich I/O for the ‘NeXML’ Format
• RNifti-1.3.1 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’
• RPMM-1.25 Recursively Partitioned Mixture Model
• RPostgreSQL-0.7-3 R Interface to the ‘PostgreSQL’ Database System
• RPresto-1.3.7 DBI Connector to Presto
• RProtoBufLib-2.6.0 C++ headers and static libraries of Protocol buffers
• RSNNS-0.4-14 Neural Networks using the Stuttgart Neural Network Simulator (SNNS)
• RSQLite-2.2.8 SQLite Interface for R
• RSclient-0.7-6 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
• Rcgmin-2013-2.21 Conjugate Gradient Minimization of Nonlinear Functions with Box Constraints
• Rcpp-1.0.7 Seamless R and C++ Integration
• RcppAnnoy-0.0.19 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest Neighbors
• RcppArmadillo-0.10.7.0.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra Library
• RcppCCTZ-0.2.9 ‘Rcpp’ Bindings for the ‘CCTZ’ Library
• RcppDate-0.0.3 ‘date’ C++ Header Library for Date and Time Functionality
• RcppEigen-0.3.3.9.1 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra Library
• RcppGSL-0.3.10 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and Matrices
• RcppHNSW-0.3.0 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest Neighbors
• RcppNumerical-0.4-0 ‘Rcpp’ Integration for Numerical Computing Libraries
• RcppParallel-5.1.4 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
• RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG Implementations
• Rdpack-2.1.2 Update and Manipulate Rd Documentation Objects
• Rdsdp-1.0.5.1 R Interface to DSDP Semidefinite Programming Library
• RefFreeEWAS-2.2 EWAS using Reference-Free DNA Methylation Mixture Deconvolution
• ReportingTools-2.34.0 Tools for making reports in various formats
• Rfast-2.0.3 A Collection of Efficient and Extremely Fast R Functions
• Rglpk-0.6-4 R/GNU Linear Programming Kit Interface
• Rgraphviz-2.38.0 Provides plotting capabilities for R graph objects
• Rhdf5lib-1.16.0 hdf5 library as an R package
• Rhpc-0.21-247 Permits *apply() Style Dispatch for ‘HPC’
• Rhtslib-1.26.0 HTSlib high-throughput sequencing library as an R package
• Ringo-1.58.0 R Investigation of ChIP-chip Oligoarrays
• Rlabkey-2.8.1 Data Exchange Between R and ‘LabKey’ Server
• Rmpi-0.6-9.2 Interface (Wrapper) to MPI (Message-Passing Interface)
• Rook-1.1-1 Rook - a web server interface for R
• Rsamtools-2.10.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
• Rserve-1.7-3.1 Binary R server
• Rsolnp-1.16 General Non-Linear Optimization
• Rssa-1.0.4 A Collection of Methods for Singular Spectrum Analysis
• Rsubread-2.8.1 Mapping, quantification and variant analysis of sequencing data
• Rtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
• Rttf2pt1-1.3.9 ‘ttf2pt1’ Program
• Rvmmin-2018-4.17.1 Variable Metric Nonlinear Function Minimization
• S4Vectors-0.32.3 Foundation of vector-like and list-like containers in Bioconductor
• SBdecomp-1.1 Estimation of the Proportion of SB Explained by Confounders
• 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-1.28.0 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-2.46.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
• SQUAREM-2021.1 Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms
• ScaledMatrix-1.2.0 Creating a DelayedMatrix of Scaled and Centered Values
• SemiPar-1.0-4.2 Semiparametic Regression
• SeqArray-1.34.0 Data management of large-scale whole-genome sequence variant calls
• SeqVarTools-1.32.0 Tools for variant data
• ShortRead-1.52.0 FASTQ input and manipulation
• SignifReg-4.2 Consistent Significance Controlled Variable Selection in Generalized Linear Regression
• SimSeq-1.4.0 Nonparametric Simulation of RNA-Seq Data
• SingleCellExperiment-1.16.0 S4 Classes for Single Cell Data
• SnowballC-0.7.0 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 Library
• SparseM-1.81 Sparse Linear Algebra
• StanHeaders-2.21.0-7 C++ Header Files for Stan
• SummarizedExperiment-1.24.0 SummarizedExperiment container
• SuperLearner-2.0-28 Super Learner Prediction
• SuppDists-1.1-9.5 Supplementary Distributions
• TFBSTools-1.32.0 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-1.1-0 TH’s Data Archive
• TMB-1.7.22 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-1.32.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
• TraMineR-2.2-2 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
• V8-3.4.2 Embedded JavaScript and WebAssembly Engine for R
• VGAM-1.1-5 Vector Generalized Linear and Additive Models
• VIM-6.1.1 Visualization and Imputation of Missing Values
• VSURF-1.1.0 Variable Selection Using Random Forests
• VariantAnnotation-1.40.0 Annotation of Genetic Variants
• VennDiagram-1.7.0 Generate High-Resolution Venn and Euler Plots
• WeightSVM-1.7-9 Subject Weighted Support Vector Machines
• WikidataQueryServiceR-1.0.0 API Client Library for ‘Wikidata Query Service’
• WikidataR-2.3.1 Read-Write API Client Library for Wikidata
• WikipediR-1.5.0 A MediaWiki API Wrapper
• Wrench-1.12.0 Wrench normalization for sparse count data
• WriteXLS-6.3.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS) and Excel 2007 (XLSX) Files
• XML-3.99-0.8 Tools for Parsing and Generating XML Within R and S-Plus
• XVector-0.34.0 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
• ade4-1.7-18 Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
• admisc-0.20 Adrian Dusa’s Miscellaneous
• affxparser-1.66.0 Affymetrix File Parsing SDK
• affy-1.72.0 Methods for Affymetrix Oligonucleotide Arrays
• affycoretools-1.66.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
• affyio-1.64.0 Tools for parsing Affymetrix data files
• aggregation-1.0.1 p-Value Aggregation Methods
• akima-0.6-2.2 Interpolation of Irregularly and Regularly Spaced Data
• alabama-2015.3-1 Constrained Nonlinear Optimization
• alr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Edition
• amap-0.8-18 Another Multidimensional Analysis Package
• animation-2.7 A Gallery of Animations in Statistics and Utilities to Create Animations
• annaffy-1.66.0 Annotation tools for Affymetrix biological metadata
• annotate-1.72.0 Annotation for microarrays
• aod-1.3.1 Analysis of Overdispersed Data
• ape-5.5 Analyses of Phylogenetics and Evolution
• apeglm-1.16.0 Approximate posterior estimation for GLM coefficients
• aplot-0.1.1 Decorate a ‘ggplot’ with Associated Information
• argparse-2.1.2 Command Line Optional and Positional Argument Parser
• argparser-0.7.1 Command-Line Argument Parser
• arm-1.12-2 Data Analysis Using Regression and Multilevel/Hierarchical Models
• arsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical Summaries
• arules-1.7-1 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-1.1.16 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-0.0-3 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-0.0-4 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
• audio-0.1-8 Audio Interface for R
• aws-2.5-1 Adaptive Weights Smoothing
• 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
• awsMethods-1.1-1 Class and Methods Definitions for Packages ‘aws’, ‘adimpro’, ‘fmri’, ‘dwi’
• babelgene-21.4 Gene Orthologs for Model Organisms in a Tidy Data Format
• backports-1.3.0 Reimplementations of Functions Introduced Since R-3.0.0
• bacr-1.0.1 Bayesian Adjustment for Confounding
• bamsignals-1.26.0 Extract read count signals from bam files
• bartMachine-1.2.6 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
• batchmeans-1.0-4 Consistent Batch Means Estimation of Monte Carlo Standard Errors
• batchtools-0.9.15 Tools for Computation on Batch Systems
• baySeq-2.28.0 Empirical Bayesian analysis of patterns of differential expression in count data
• bayesm-3.1-4 Bayesian Inference for Marketing/Micro-Econometrics
• bayesplot-1.8.1 Plotting for Bayesian Models
• bbmle-1.0.24 Tools for General Maximum Likelihood Estimation
• bdsmatrix-1.3-4 Routines for Block Diagonal Symmetric Matrices
• beachmat-2.10.0 Compiling Bioconductor to Handle Each Matrix Type
• beanplot-1.2 Visualization via Beanplots (Like Boxplot/Stripchart/Violin Plot)
• beeswarm-0.4.0 The Bee Swarm Plot, an Alternative to Stripchart
• benchmark-0.3-6 Benchmark Experiments Toolbox
• betareg-3.1-4 Beta Regression
• 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-2.4-2 Biological Structure Analysis
• biom-0.3.12 An interface package (beta) for the BIOM file format.
• biomaRt-2.50.1 Interface to BioMart databases (i.e. Ensembl)
• biomformat-1.22.0 An interface package for the BIOM file format
• biomod2-3.5.1 Ensemble Platform for Species Distribution Modeling
• biovizBase-1.42.0 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-1.0-7 Bitwise Operations
• blavaan-0.3-17 Bayesian Latent Variable Analysis
• blob-1.2.2 A Simple S3 Class for Representing Vectors of Binary Data (‘BLOBS’)
• bmp-0.3 Read Windows Bitmap (BMP) Images
• bnlearn-4.7 Bayesian Network Structure Learning, Parameter Learning and Inference
• bold-1.2.0 Interface to Bold Systems API
• bookdown-0.24 Authoring Books and Technical Documents with R Markdown
• boot-1.3-28 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-0.7.2 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-1.1-2 Bridge Sampling for Marginal Likelihoods and Bayes Factors
• brio-1.1.2 Basic R Input Output
• brms-2.16.1 Bayesian Regression Models using ‘Stan’
• broom-0.7.10 Convert Statistical Objects into Tidy Tibbles
• broom.helpers-1.4.0 Helpers for Model Coefficients Tibbles
• broom.mixed-0.2.7 Tidying Methods for Mixed Models
• bslib-0.3.1 Custom ‘Bootstrap’ ‘Sass’ Themes for ‘shiny’ and ‘rmarkdown’
• bst-0.3-23 Gradient Boosting
• bumphunter-1.36.0 Bump Hunter
• cNORM-2.1.0 Continuous Norming
• cSEM-0.4.0 Composite-Based Structural Equation Modeling
• caTools-1.18.2 Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
• cachem-1.0.6 Cache R Objects with Automatic Pruning
• calibrate-1.7.7 Calibration of Scatterplot and Biplot Axes
• callr-3.7.0 Call R from R
• car-3.0-11 Companion to Applied Regression
• carData-3.0-4 Companion to Applied Regression Data Sets
• caret-6.0-90 Classification and Regression Training
• catdata-1.2.2 Categorical Data
• 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.
• checkmate-2.0.0 Fast and Versatile Argument Checks
• chemometrics-1.4.2 Multivariate Statistical Analysis in Chemometrics
• chipseq-1.44.0 chipseq: A package for analyzing chipseq data
• chromVAR-1.16.0 Chromatin Variation Across Regions
• chron-2.3-56 Chronological Objects which can Handle Dates and Times
• circlize-0.4.13 Circular Visualization
• circular-0.4-93 Circular Statistics
• clValid-0.7 Validation of Clustering Results
• class-7.3-19 Functions for Classification
• classInt-0.4-3 Choose Univariate Class Intervals
• cli-3.1.0 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-0.3-60 Cluster Ensembles
• cluster-2.1.2 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et al.
• clusterGeneration-1.3.7 Random Cluster Generation (with Specified Degree of Separation)
• clusterProfiler-4.2.0 A universal enrichment tool for interpreting omics data
• clusterRepro-0.9 Reproducibility of Gene Expression Clusters
• clustree-0.4.3 Visualise Clusterings at Different Resolutions
• cobalt-4.3.1 Covariate Balance Tables and Plots
• 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-1.4-2 Conditional Inference Procedures in a Permutation Test Framework
• colorRamps-2.3 Builds Color Tables
• colorspace-2.0-2 A Toolbox for Manipulating and Assessing Colors and Palettes
• colourpicker-1.1.1 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
• compiler built in
• compositions-2.0-2 Compositional Data Analysis
• conditionz-0.1.0 Control How Many Times Conditions are Thrown
• config-0.3.1 Manage Environment Specific Configuration Values
• conflicted-1.0.4 An Alternative Conflict Resolution Strategy
• conquer-1.2.0 Convolution-Type Smoothed Quantile Regression
• copCAR-2.0-4 Fitting the copCAR Regression Model for Discrete Areal Data
• copula-1.0-1 Multivariate Dependence with Copulas
• copynumber-1.34.0 Segmentation of single- and multi-track copy number data by penalized least squares regression.
• corpcor-1.6.10 Efficient Estimation of Covariance and (Partial) Correlation
• corrplot-0.90 Visualization of a Correlation Matrix
• covr-3.5.1 Test Coverage for Packages
• cowplot-1.1.1 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’
• coxed-0.3.3 Duration-Based Quantities of Interest for the Cox Proportional Hazards Model
• coxme-2.2-16 Mixed Effects Cox Models
• cpp11-0.4.0 A C++11 Interface for R’s C Interface
• crayon-1.4.2 Colored Terminal Output
• credentials-1.3.1 Tools for Managing SSH and Git Credentials
• crosstalk-1.1.1 Inter-Widget Interactivity for HTML Widgets
• crul-1.1.0 HTTP Client
• csSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarrays
• ctmle-0.1.2 Collaborative Targeted Maximum Likelihood Estimation
• cubature-2.0.4.2 Adaptive Multivariate Integration over Hypercubes
• cubelyr-1.0.1 A Data Cube ‘dplyr’ Backend
• cummeRbund-2.36.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
• curl-4.3.2 A Modern and Flexible Web Client for R
• curry-0.1.1 Partial Function Application with %<%, %-<%, and %><%
• cvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervals
• cyclocomp-1.1.0 Cyclomatic Complexity of R Code
• cytolib-2.6.0 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
• dada2-1.22.0 Accurate, high-resolution sample inference from amplicon sequencing data
• data.table-1.14.2 Extension of data.frame
• data.tree-1.0.0 General Purpose Hierarchical Data Structure
• datasets built in
• dbarts-0.9-20 Discrete Bayesian Additive Regression Trees Sampler
• dbplyr-2.1.1 A ‘dplyr’ Back End for Databases
• dbscan-1.1-8 Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms
• ddalpha-1.3.11 Depth-Based Classification and Calculation of Data Depth
• deSolve-1.30 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-1.0-6 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
• dendextend-1.15.2 Extending ‘dendrogram’ Functionality in R
• derfinder-1.28.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
• derfinderHelper-1.28.0 derfinder helper package
• desc-1.4.0 Manipulate DESCRIPTION Files
• descr-1.1.5 Descriptive Statistics
• devtools-2.4.2 Tools to Make Developing R Packages Easier
• dfidx-0.0-4 Indexed Data Frames
• dfoptim-2020.10-1 Derivative-Free Optimization
• diagram-1.6.5 Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams
• dials-0.0.10 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-0.3.5 Diffs for R Objects
• diffusionMap-1.2.0 Diffusion Map
• digest-0.6.28 Create Compact Hash Digests of R Objects
• dimRed-0.2.3 A Framework for Dimensionality Reduction
• diptest-0.76-0 Hartigan’s Dip Test Statistic for Unimodality - Corrected
• dismo-1.3-5 Species Distribution Modeling
• distillery-1.2-1 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’
• distributional-0.2.2 Vectorised Probability Distributions
• diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis Package
• doBy-4.6.11 Groupwise Statistics, LSmeans, Linear Estimates, 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
• dotCall64-1.0-1 Enhanced Foreign Function Interface Supporting Long Vectors
• downloader-0.4 Download Files over HTTP and HTTPS
• dplyr-1.0.7 A Grammar of Data Manipulation
• dqrng-0.3.0 Fast Pseudo Random Number Generators
• dr-3.0.10 Methods for Dimension Reduction for Regression
• drc-3.0-1 Analysis of Dose-Response Curves
• 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-1.1.0 Data Table Back-End for ‘dplyr’
• 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
• e1071-1.7-9 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
• earth-5.3.1 Multivariate Adaptive Regression Splines
• edgeR-3.36.0 Empirical Analysis of Digital Gene Expression Data in R
• elasticnet-1.3 Elastic-Net for Sparse Estimation and Sparse PCA
• elementR-1.3.7 An Framework for Reducing Elemental LAICPMS Data from Solid Structures
• ellipse-0.4.2 Functions for Drawing Ellipses and Ellipse-Like Confidence Regions
• ellipsis-0.3.2 Tools for Working with …
• emdbook-1.3.12 Support Functions and Data for “Ecological Models and Data”
• emulator-1.2-21 Bayesian Emulation of Computer Programs
• energy-1.7-8 E-Statistics: Multivariate Inference via the Energy of Data
• enrichplot-1.14.1 Visualization of Functional Enrichment Result
• ensembldb-2.18.2 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-4.1.2 Fit, Simulate and Diagnose Exponential-Family Models for Networks
• ergm.count-4.0.2 Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
• etrunct-0.1 Computes Moments of Univariate Truncated t Distribution
• europepmc-0.4.1 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-0.999-6 Matrix Exponential, Log, ‘etc’
• expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
• extRemes-2.1-1 Extreme Value Analysis
• extrafont-0.17 Tools for Using Fonts
• extrafontdb-1.0 Package for holding the database for the extrafont package
• fANCOVA-0.6-1 Nonparametric Analysis of Covariance
• fail-1.3 File Abstraction Interface Layer (FAIL)
• fansi-0.5.0 ANSI Control Sequence Aware String Functions
• faraway-1.0.7 Functions and Datasets for Books by Julian Faraway
• farver-2.1.0 High Performance Colour Space Manipulation
• fastICA-1.2-3 FastICA Algorithms to Perform ICA and Projection Pursuit
• fastcluster-1.2.3 Fast Hierarchical Clustering Routines for R and ‘Python’
• fasterize-1.0.3 Fast Polygon to Raster Conversion
• fastmap-1.1.0 Fast Data Structures
• fastmatch-1.1-3 Fast ‘match()’ Function
• fastseg-1.40.0 fastseg - a fast segmentation algorithm
• fasttime-1.0-2 Fast Utility Function for Time Parsing and Conversion
• fda-5.5.1 Functional Data Analysis
• fdrtool-1.2.16 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-4.0.5 Memory-Efficient Storage of Large Data on Disk and Fast Access Functions
• ffbase-0.13.3 Basic Statistical Functions for Package ‘ff’
• fftw-1.0-6 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-1.20.0 Fast Gene Set Enrichment Analysis
• fields-13.3 Tools for Spatial Data
• filehash-2.4-2 Simple Key-Value Database
• filelock-1.0.2 Portable File Locking
• finalfit-1.0.3 Quickly Create Elegant Regression Results Tables and Plots when Modelling
• findpython-1.0.7 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-1.1-6 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-3.32.0 Clustering for Flow Cytometry
• flowCore-2.6.0 flowCore: Basic structures for flow cytometry data
• flowStats-4.6.0 Statistical methods for the analysis of flow cytometry data
• flowViz-1.58.0 Visualization for flow cytometry
• flowWorkspace-4.6.0 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)
• fmri-1.9.6 Analysis of fMRI Experiments
• fontawesome-0.2.2 Easily Work with ‘Font Awesome’ Icons
• forcats-0.5.1 Tools for Working with Categorical Variables (Factors)
• foreach-1.5.1 Provides Foreach Looping Construct
• forecast-8.15 Forecasting Functions for Time Series and Linear Models
• foreign-0.8-81 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, ‘dBase’, …
• forestplot-2.0.1 Advanced Forest Plot Using ‘grid’ Graphics
• forge-0.2.0 Casting Values into Shape
• formatR-1.11 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-0.2.3 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-1.23.0 Unified Parallel and Distributed Processing in R for Everyone
• future.apply-1.8.1 Apply Function to Elements in Parallel using Futures
• gWidgets2-1.0-8 Rewrite of gWidgets API for Simplified GUI Construction
• gWidgets2tcltk-1.0-6 Toolkit Implementation of gWidgets2 for tcltk
• gage-2.44.0 Generally Applicable Gene-set Enrichment for Pathway Analysis
• gam-1.20 Generalized Additive Models
• gamlss-5.3-4 Generalised Additive Models for Location Scale and Shape
• gamlss.data-6.0-1 Data for Generalised Additive Models for Location Scale and Shape
• gamlss.dist-5.3-2 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-1.2.3-1 Genetic Analysis Package
• gapfill-0.9.6-1 Fill Missing Values in Satellite Data
• gargle-1.2.0 Utilities for Working with Google APIs
• gaussquad-1.0-2 Collection of functions for Gaussian quadrature
• 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-2.66.0 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-1.30.0
• gdtools-0.2.3 Utilities for Graphical Rendering
• gee-4.13-20 Generalized Estimation Equation Solver
• geepack-1.3-2 Generalized Estimating Equation Package
• geiger-2.0.7 Analysis of Evolutionary Diversification
• geneLenDataBase-1.30.0 Lengths of mRNA transcripts for a number of genomes
• genefilter-1.76.0 genefilter: methods for filtering genes from high-throughput experiments
• geneplotter-1.72.0 Graphics related functions for Bioconductor
• generics-0.1.1 Common S3 Generics not Provided by Base R Methods Related to Model Fitting
• geometry-0.4.5 Mesh Generation and Surface Tessellation
• gert-1.4.1 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-1.42.0 Visualization tools for genomic data
• ggcyto-1.22.0 Visualize Cytometry data with ggplot
• ggdendro-0.1.22 Create Dendrograms and Tree Diagrams Using ‘ggplot2’
• ggfan-0.1.3 Summarise a Distribution Through Coloured Intervals
• ggforce-0.3.3 Accelerating ‘ggplot2’
• ggfun-0.0.4 Miscellaneous Functions for ‘ggplot2’
• ggnetwork-0.5.10 Geometries to Plot Networks with ‘ggplot2’
• ggnewscale-0.4.5 Multiple Fill and Colour Scales in ‘ggplot2’
• ggplot2-3.3.5 Create Elegant Data Visualisations Using the Grammar of Graphics
• ggplotify-0.1.0 Convert Plot to ‘grob’ or ‘ggplot’ Object
• ggpointdensity-0.1.0 A Cross Between a 2D Density Plot and a Scatter Plot
• ggpubr-0.4.0 ‘ggplot2’ Based Publication Ready Plots
• ggraph-2.0.5 An Implementation of Grammar of Graphics for Graphs and Networks
• ggrepel-0.9.1 Automatically Position Non-Overlapping Text Labels with ‘ggplot2’
• ggridges-0.5.3 Ridgeline Plots in ‘ggplot2’
• ggsci-2.9 Scientific Journal and Sci-Fi Themed Color Palettes for ‘ggplot2’
• ggsignif-0.6.3 Significance Brackets for ‘ggplot2’
• ggthemes-4.2.4 Extra Themes, Scales and Geoms for ‘ggplot2’
• ggtree-3.2.1 an R package for visualization of tree and annotation data
• ggvis-0.4.7 Interactive Grammar of Graphics
• gh-1.3.0 ‘GitHub’ ‘API’
• git2r-0.28.0 Provides Access to Git Repositories
• gitcreds-0.1.1 Query ‘git’ Credentials from ‘R’
• glasso-1.11 Graphical Lasso: Estimation of Gaussian Graphical Models
• gld-2.6.2 Estimation and Use of the Generalised (Tukey) Lambda Distribution
• gllvm-1.3.1 Generalized Linear Latent Variable Models
• glmmML-1.1.1 Generalized Linear Models with Clustering
• glmmTMB-1.1.2.3 Generalized Linear Mixed Models using Template Model Builder
• glmnet-4.1-2 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-1.6-6 Generalized Method of Moments and Generalized Empirical Likelihood
• gmodels-2.18.1 Various R Programming Tools for Model Fitting
• gmp-0.6-2 Multiple Precision Arithmetic
• gnumeric-0.7-8 Read Data from Files Readable by ‘gnumeric’
• goftest-1.2-3 Classical Goodness-of-Fit Tests for Univariate Distributions
• gomms-1.0 GLM-Based Ordination Method
• googledrive-2.0.0 An Interface to Google Drive
• googlesheets4-1.0.0 Access Google Sheets using the Sheets API V4
• goseq-1.46.0 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-1.72.0 graph: A package to handle graph data structures
• graphics built in
• graphlayouts-0.7.1 Additional Layout Algorithms for Network Visualizations
• grf-2.0.2 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-3.4.0 Regularization Paths for Regression Models with Grouped Covariates
• gsalib-2.1 Utility Functions For GATK
• gsl-2.1-7 Wrapper for the Gnu Scientific Library
• gsubfn-0.7 Utilities for Strings and Function Arguments
• gsw-1.0-6 Gibbs Sea Water Functions
• gt-0.3.1 Easily Create Presentation-Ready Display Tables
• gtable-0.3.0 Arrange ‘Grobs’ in Tables
• gtools-3.9.2 Various R Programming Tools
• gtsummary-1.5.0 Presentation-Ready Data Summary and Analytic Result Tables
• h2o-3.34.0.3 R Interface for the ‘H2O’ Scalable Machine Learning Platform
• hal9001-0.4.1 The Scalable Highly Adaptive Lasso
• hapassoc-1.2-8 Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
• haplo.stats-1.8.7 Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
• hardhat-0.1.6 Construct Modeling Packages
• haven-2.4.3 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files
• hdf5r-1.3.4 Interface to the ‘HDF5’ Binary Data Format
• hdm-0.3.1 High-Dimensional Metrics
• hdrcde-3.4 Highest Density Regions and Conditional Density Estimation
• heatmap3-1.1.9 An Improved Heatmap Package
• here-1.0.1 A Simpler Way to Find Your Files
• hexbin-1.28.2 Hexagonal Binning Routines
• hgu133plus2.db-3.13.0 Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)
• highr-0.9 Syntax Highlighting for R Source Code
• hms-1.1.1 Pretty Time of Day
• hopach-2.54.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
• htmlTable-2.3.0 Advanced Tables for Markdown/HTML
• htmltools-0.5.2 Tools for HTML
• htmlwidgets-1.5.4 HTML Widgets for R
• httpcode-0.3.0 ‘HTTP’ Status Code Helper
• httpuv-1.6.3 HTTP and WebSocket Server Library
• httr-1.4.2 Tools for Working with URLs and HTTP
• huge-1.3.5 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
• ids-1.0.1 Generate Random Identifiers
• ie2misc-0.8.6 Irucka Embry’s Miscellaneous USGS Functions
• igraph-1.2.7 Network Analysis and Visualization
• igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
• illuminaio-0.36.0 Parsing Illumina Microarray Output Files
• image.binarization-0.1.2 Binarize Images for Enhancing Optical Character Recognition
• imager-0.42.10 Image Processing Library Based on ‘CImg’
• imagerExtra-1.3.2 Extra Image Processing Library Based on ‘imager’
• impute-1.68.0 impute: Imputation for microarray data
• ineq-0.2-13 Measuring Inequality, Concentration, and Poverty
• infer-1.0.0 Tidy Statistical Inference
• inferference-1.0.2 Methods for Causal Inference with Interference
• influenceR-0.1.0.1 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-0.3.19 Functions to Inline C, C++, Fortran Function Calls from R
• interactiveDisplayBase-1.32.0 Base package for enabling powerful shiny web displays of Bioconductor objects
• intergraph-2.0-2 Coercion Routines for Network Data Objects
• interpretR-0.2.4 Binary Classifier and Regression Model Interpretation Functions
• intrinsicDimension-1.2.0 Intrinsic Dimension Estimation
• inum-1.0-4 Interval and Enum-Type Representation of Vectors
• invgamma-1.1 The Inverse Gamma Distribution
• iotools-0.3-2 I/O Tools for Streaming
• ipred-0.9-12 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-0.2.5 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-0.1-9 Read and write JPEG images
• jquerylib-0.1.4 Obtain ‘jQuery’ as an HTML Dependency Object
• jsonlite-1.7.2 A Simple and Robust JSON Parser and Generator for R
• jstable-1.0.7 Create Tables from Different Types of Regression
• karyoploteR-1.20.0 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
• keyring-1.2.0 Access the System Credential Store from R
• kin.cohort-0.7 Analysis of Kin-Cohort Studies
• kinship2-1.8.5 Pedigree Functions
• klaR-0.6-15 Classification and Visualization
• knitr-1.36 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-1.13.2 Kernel Smoothing
• kyotil-2021.5-14 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-2.9.0 Manipulating Labelled Data
• laeken-0.5.2 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
• lasso2-1.2-22 L1 Constrained Estimation aka `lasso’
• lassosum 0.4.5
• latentnet-2.10.5 Latent Position and Cluster Models for Statistical Networks
• later-1.3.0 Utilities for Scheduling Functions to Execute Later with Event Loops
• lattice-0.20-45 Trellis Graphics for R
• latticeExtra-0.6-29 Extra Graphical Utilities Based on Lattice
• lava-1.6.10 Latent Variable Models
• lavaan-0.6-9 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-0.3.9 R Implementation of Leiden Clustering Algorithm
• lhs-1.1.3 Latin Hypercube Samples
• libcoin-1.0-9 Linear Test Statistics for Permutation Inference
• lifecycle-1.0.1 Manage the Life Cycle of your Package Functions
• limSolve-1.5.6 Solving Linear Inverse Models
• limma-3.50.0 Linear Models for Microarray Data
• linkcomm-1.0-14 Tools for Generating, Visualizing, and Analysing Link Communities in Networks
• 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
• lme4-1.1-27.1 Linear Mixed-Effects Models using ‘Eigen’ and S4
• lmerTest-3.1-3 Tests in Linear Mixed Effects Models
• lmom-2.8 L-Moments
• lmtest-0.9-38 Testing Linear Regression Models
• lobstr-1.1.1 Visualize R Data Structures with Trees
• locfdr-1.1-8 Computes Local False Discovery Rates
• locfit-1.5-9.4 Local Regression, Likelihood and Density Estimation
• logcondens-2.1.6 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-1.1-9 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
• lpSolveAPI-5.5.2.0-17.7 R Interface to ‘lp_solve’ Version 5.5.2.0
• lpridge-1.0-8 Local Polynomial (Ridge) Regression
• lpsymphony-1.22.0 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
• lslx-0.6.10 Semi-Confirmatory Structural Equation Modeling via Penalized Likelihood or Least Squares
• lubridate-1.8.0 Make Dealing with Dates a Little Easier
• lumi-2.46.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
• lwgeom-0.2-8 Bindings to Selected ‘liblwgeom’ Functions for Simple Features
• mRMRe-2.1.2 Parallelized Minimum Redundancy, Maximum Relevance (mRMR)
• maSigPro-1.66.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
• magic-1.5-9 Create and Investigate Magic Squares
• magick-2.7.3 Advanced Graphics and Image-Processing in R
• magrittr-2.0.1 A Forward-Pipe Operator for R
• manipulateWidget-0.11.1 Add Even More Interactivity to Interactive Charts
• mapdata-2.3.0 Extra Map Databases
• mapproj-1.2.7 Map Projections
• maps-3.4.0 Draw Geographical Maps
• maptools-1.1-2 Tools for Handling Spatial Objects
• markdown-1.1 Render Markdown with the C Library ‘Sundown’
• marray-1.72.0 Exploratory analysis for two-color spotted microarray data
• mathjaxr-1.4-0 Using ‘Mathjax’ in Rd Files
• matrixStats-0.61.0 Functions that Apply to Rows and Columns of Matrices (and to Vectors)
• matrixcalc-1.0-5 Collection of Functions for Matrix Calculations
• maxLik-1.5-2 Maximum Likelihood Estimation and Related Tools
• maxlike-0.1-8 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-2.9-5 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
• mcmcse-1.5-0 Monte Carlo Standard Errors for MCMC
• mda-0.5-2 Mixture and Flexible Discriminant Analysis
• medflex-0.6-7 Flexible Mediation Analysis Using Natural Effect Models
• mediation-4.5.0 Causal Mediation Analysis
• memoise-2.0.0 ‘Memoisation’ of Functions
• memuse-4.2-1 Memory Estimation Utilities
• metafor-3.0-2 Meta-Analysis Package for R
• metagenomeSeq-1.36.0 Statistical analysis for sparse high-throughput sequencing
• methods built in
• methylKit-1.20.0 DNA methylation analysis from high-throughput bisulfite sequencing results
• methylumi-2.40.1 Handle Illumina methylation data
• mets-1.2.9 Analysis of Multivariate Event Times
• mgcv-1.8-38 Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
• mgsub-1.7.3 Safe, Multiple, Simultaneous String Substitution
• mhsmm-0.4.16 Inference for Hidden Markov and Semi-Markov Models
• mi-1.0 Missing Data Imputation and Model Checking
• mice-3.13.0 Multivariate Imputation by Chained Equations
• miceadds-3.11-6 Some Additional Multiple Imputation Functions, Especially for ‘mice’
• microbenchmark-1.4.9 Accurate Timing Functions
• mime-0.12 Map Filenames to MIME Types
• minerva-1.5.10 Maximal Information-Based Nonparametric Exploration for Variable Analysis
• minfi-1.40.0 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-0.9-1 Miscellaneous 3D Plots
• miscTools-0.6-26 Miscellaneous Tools and Utilities
• missForest-1.4 Nonparametric Missing Value Imputation using Random Forest
• mitml-0.4-3 Tools for Multiple Imputation in Multilevel Modeling
• mitools-2.4 Tools for Multiple Imputation of Missing Data
• mixOmics-6.18.1 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-2.1-3 Machine Learning Benchmark Problems
• mlegp-3.1.8 Maximum Likelihood Estimates of Gaussian Processes
• mlogit-1.1-1 Multinomial Logit Models
• mlr-2.19.0 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-0.1.1 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-0.10.02 Keep Track of Dates in Terms of Months
• motifmatchr-1.16.0 Fast Motif Matching in R
• mpath-0.4-2.19 Regularized Linear Models
• msa-1.26.0 Multiple Sequence Alignment
• msigdbr-7.4.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
• msm-1.6.9 Multi-State Markov and Hidden Markov Models in Continuous Time
• multcomp-1.4-17 Simultaneous Inference in General Parametric Models
• multicool-0.1-12 Permutations of Multisets in Cool-Lex Order
• multipol-1.0-7 Multivariate Polynomials
• multtest-2.50.0 Resampling-based multiple hypothesis testing
• munsell-0.5.0 Utilities for Using Munsell Colours
• mvabund-4.1.12 Statistical Methods for Analysing Multivariate Abundance Data
• mvnfast-0.2.7 Fast Multivariate Normal and Student’s t Methods
• mvtnorm-1.1-3 Multivariate Normal and t Distributions
• nabor-0.5.0 Wraps ‘libnabo’, a Fast K Nearest Neighbour Library for Low Dimensions
• naniar-0.6.1 Data Structures, Summaries, and Visualisations for Missing Data
• nanotime-0.3.4 Nanosecond-Resolution Time Support for R
• natserv-1.0.0 ‘NatureServe’ Interface
• naturalsort-0.1.3 Natural Ordering
• 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-2.40.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
• ndtv-0.13.2 Network Dynamic Temporal Visualizations
• network-1.17.1 Classes for Relational Data
• networkDynamic-0.11.0 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
• 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-3.3.2 Solve Systems of Nonlinear Equations
• nlme-3.1-153 Linear and Nonlinear Mixed Effects Models
• nloptr-1.2.2.2 R Interface to NLopt
• nlsem-0.8 Fitting Structural Equation Mixture Models
• nnet-7.3-16 Feed-Forward Neural Networks and Multinomial Log-Linear Models
• nnls-1.4 The Lawson-Hanson algorithm for non-negative least squares<U+000a>(NNLS)
• nonnest2-0.5-5 Tests of Non-Nested Models
• nor1mix-1.3-0 Normal aka Gaussian (1-d) Mixture Models (S3 Classes and Methods)
• norm-1.0-9.5 Analysis of Multivariate Normal Datasets with Missing Values
• nortest-1.0-4 Tests for Normality
• np-0.60-11 Nonparametric Kernel Smoothing Methods for Mixed Data Types
• npsurv-0.5-0 Nonparametric Survival Analysis
• numDeriv-2016.8-1.1 Accurate Numerical Derivatives
• numbers-0.8-2 Number-Theoretic Functions
• nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
• oai-0.3.2 General Purpose ‘Oai-PMH’ Services Client
• oce-1.4-0 Analysis of Oceanographic Data
• odbc-1.3.2 Connect to ODBC Compatible Databases (using the DBI Interface)
• oddsratio-2.0.1 Odds Ratio Calculation for GAM(M)s & GLM(M)s
• oligo-1.58.0 Preprocessing tools for oligonucleotide arrays
• oligoClasses-1.56.0 Classes for high-throughput arrays supported by oligo and crlmm
• openCyto-2.6.0 Hierarchical Gating Pipeline for flow cytometry data
• openssl-1.4.5 Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
• openxlsx-4.2.4 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
• optimr-2019-12.16 A Replacement and Extension of the ‘optim’ Function
• optimx-2021-10.12 Expanded Replacement and Extension of the ‘optim’ Function
• optmatch-0.9-15 Functions for Optimal Matching
• optparse-1.7.1 Command Line Option Parser
• ordinal-2019.12-10 Regression Models for Ordinal Data
• org.Hs.eg.db-3.14.0 Genome wide annotation for Human
• org.Mm.eg.db-3.14.0 Genome wide annotation for Mouse
• origami-1.0.5 Generalized Framework for Cross-Validation
• oro.nifti-0.11.0 Rigorous - ‘NIfTI’ + ‘ANALYZE’ + ‘AFNI’ : Input / Output
• orthopolynom-1.0-5 Collection of Functions for Orthogonal and Orthonormal Polynomials
• osqp-0.6.0.5 Quadratic Programming Solver using the ‘OSQP’ Library
• outliers-0.14 Tests for Outliers
• pROC-1.18.0 Display and Analyze ROC Curves
• pack-0.1-1 Convert values to/from raw vectors
• packrat-0.7.0 A Dependency Management System for Projects and their R Package Dependencies
• pacman-0.5.1 Package Management Tool
• pamr-1.56.1 Pam: Prediction Analysis for Microarrays
• pan-1.6 Multiple Imputation for Multivariate Panel or Clustered Data
• parallel built in
• parallelMap-1.5.1 Unified Interface to Parallelization Back-Ends
• parallelly-1.28.1 Enhancing the ‘parallel’ Package
• parsedate-1.2.1 Recognize and Parse Dates in Various Formats, Including All ISO 8601 Formats
• parsnip-0.1.7 A Common API to Modeling and Analysis Functions
• partools-1.1.6 Tools for the ‘Parallel’ Package
• party-1.3-9 A Laboratory for Recursive Partytioning
• partykit-1.2-15 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-1.34.0 a tool set for pathway based data integration and visualization
• pbapply-1.5-0 Adding Progress Bar to ‘*apply’ Functions
• pbivnorm-0.6.0 Vectorized Bivariate Normal CDF
• pbkrtest-0.5.1 Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models
• pbs-1.1 Periodic B Splines
• pcaMethods-1.86.0 A collection of PCA methods
• pcaPP-1.9-74 Robust PCA by Projection Pursuit
• pdftools-3.0.1 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-1.3 Parallelised Estimation of Prediction Error
• perm-1.0-0.2 Exact or Asymptotic Permutation Tests
• permute-0.9-5 Functions for Generating Restricted Permutations of Data
• phangorn-2.7.1 Phylogenetic Reconstruction and Analysis
• pheatmap-1.0.12 Pretty Heatmaps
• phylobase-0.8.10 Base Package for Phylogenetic Structures and Comparative Data
• phyloseq-1.38.0 Handling and analysis of high-throughput microbiome census data
• phytools-0.7-90 Phylogenetic Tools for Comparative Biology (and Other Things)
• pillar-1.6.4 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-0.4-12 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-1.2.3 Simulate Package Installation and Attach
• pkgmaker-0.32.2 Development Utilities for R Packages
• plogr-0.2.0 The ‘plog’ C++ Logging Library
• plot3D-1.4 Plotting Multi-Dimensional Data
• plot3Drgl-1.0.2 Plotting Multi-Dimensional Data - Using ‘rgl’
• plotly-4.10.0 Create Interactive Web Graphics via ‘plotly.js’
• plotmo-3.6.1 Plot a Model’s Residuals, Response, and Partial Dependence Plots
• plotrix-3.8-2 Various Plotting Functions
• pls-2.8-0 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
• poLCA-1.4.1 Polytomous Variable Latent Class Analysis
• 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
• polycor-0.7-10 Polychoric and Polyserial Correlations
• polyester-1.30.0 Simulate RNA-seq reads
• polynom-1.4-0 A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations
• posterior-1.1.0 Tools for Working with Posterior Distributions
• 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-2.3.3 Practical Numerical Math Functions
• praise-1.0.0 Praise Users
• premessa 0.2.6
• preprocessCore-1.56.0 A collection of pre-processing functions
• preseqR-4.0.0 Predicting Species Accumulation Curves
• prettyunits-1.1.1 Pretty, Human Readable Formatting of Quantities
• processx-3.5.2 Execute and Control System Processes
• prodlim-2019.11.13 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
• progress-1.2.2 Terminal Progress Bars
• progressr-0.9.0 An Inclusive, Unifying API for Progress Updates
• projpred-2.0.2 Projection Predictive Feature Selection
• promises-1.2.0.1 Abstractions for Promise-Based Asynchronous Programming
• proto-1.0.0 Prototype Object-Based Programming
• proxy-0.4-26 Distance and Similarity Measures
• pryr-0.1.5 Tools for Computing on the Language
• ps-1.6.0 List, Query, Manipulate System Processes
• pscl-1.5.5 Political Science Computational Laboratory
• pspline-1.0-18 Penalized Smoothing Splines
• psych-2.1.9 Procedures for Psychological, Psychometric, and Personality Research
• psychotools-0.7-0 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-1.3.3 Smooth Additive Quantile Regression Models
• qgraph-1.9 Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
• qpdf-1.1 Split, Combine and Compress PDF Files
• qqman-0.1.8 Q-Q and Manhattan Plots for GWAS Data
• qrnn-2.0.5 Quantile Regression Neural Network
• qtl-1.50 Tools for Analyzing QTL Experiments
• quadprog-1.5-8 Functions to Solve Quadratic Programming Problems
• quantmod-0.4.18 Quantitative Financial Modelling Framework
• quantoptr-0.1.3 Algorithms for Quantile- And Mean-Optimal Treatment Regimes
• quantreg-5.86 Quantile Regression
• quantsmooth-1.60.0 Quantile smoothing and genomic visualization of array data
• questionr-0.7.5 Functions to Make Surveys Processing Easier
• qvalue-2.26.0 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-2.42.0 de novo motif discovery
• rJava-1.0-5 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-2.13.0 Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
• rangeModelMetadata-0.1.4 Provides Templates for Metadata Files Associated with Species Range Models
• ranger-0.13.1 A Fast Implementation of Random Forests
• rappdirs-0.3.3 Application Directories: Determine Where to Save Data, Caches, and Logs
• raster-3.5-2 Geographic Data Analysis and Modeling
• rasterVis-0.51.0 Visualization Methods for Raster Data
• ratelimitr-0.4.1 Rate Limiting for R
• rbenchmark-1.0.0 Benchmarking routine for R
• rbibutils-2.2.4 Read ‘Bibtex’ Files and Convert Between Bibliography Formats
• rbison-1.0.0 Interface to the ‘USGS’ ‘BISON’ API
• rcmdcheck-1.4.0 Run ‘R CMD check’ from ‘R’ and Capture Results
• rda-1.0.2-2.1 Shrunken Centroids Regularized Discriminant Analysis
• rdrop2-0.8.2.1 Programmatic Interface to the ‘Dropbox’ API
• readODS-1.7.0 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-2.0.2 Read Rectangular Text Data
• readxl-1.3.1 Read Excel Files
• rebird-1.3.0 R Client for the eBird Database of Bird Observations
• recipes-0.1.17 Preprocessing and Feature Engineering Steps for Modeling
• refGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from ‘Ensembl’ and ‘UCSC’ Genome Browsers
• refund-0.1-24 Regression with Functional Data
• regioneR-1.26.0 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
• regsem-1.8.0 Regularized Structural Equation Modeling
• regtools-1.1.0 Regression and Classification Tools
• relations-0.6-10 Data Structures and Algorithms for Relations
• relevent-1.1 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-2.4.1 R Package Installation from Remote Repositories, Including ‘GitHub’
• rentrez-1.2.3 ‘Entrez’ in R
• repr-1.1.3 Serializable Representations
• reprex-2.0.1 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
• restfulr-0.0.13 R Interface to RESTful Web Services
• reticulate-1.22 Interface to ‘Python’
• rex-1.2.0 Friendly Regular Expressions
• rgbif-3.6.0 Interface to the Global Biodiversity Information Facility API
• rgdal-1.5-27 Bindings for the ‘Geospatial’ Data Abstraction Library
• rgenoud-5.8-3.0 R Version of GENetic Optimization Using Derivatives
• rgeos-0.5-8 Interface to Geometry Engine - Open Source (‘GEOS’)
• rgexf-0.16.2 Build, Import and Export GEXF Graph Files
• rgl-0.107.14 3D Visualization Using OpenGL
• rhandsontable-0.3.8 Interface to the ‘Handsontable.js’ Library
• rhdf5-2.38.0 R Interface to HDF5
• rhdf5filters-1.6.0 HDF5 Compression Filters
• ridigbio-0.3.5 Interface to the iDigBio Data API
• rio-0.5.27 A Swiss-Army Knife for Data I/O
• ritis-1.0.0 Integrated Taxonomic Information System Client
• rjags-4-12 Bayesian Graphical Models using MCMC
• rjson-0.2.20 JSON for R
• rlang-0.4.12 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
• rlist-0.4.6.2 A Toolbox for Non-Tabular Data Manipulation
• rmarkdown-2.11 Dynamic Documents for R
• rmeta-3.0 Meta-Analysis
• rms-6.2-0 Regression Modeling Strategies
• rncl-0.8.4 An Interface to the Nexus Class Library
• rnetcarto-0.2.4 Fast Network Modularity and Roles Computation by Simulated Annealing (Rgraph C Library Wrapper for R)
• rngtools-1.5.2 Utility Functions for Working with Random Number Generators
• robustbase-0.93-9 Basic Robust Statistics
• rootSolve-1.8.2.3 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations
• rotl-3.0.11 Interface to the ‘Open Tree of Life’ API
• roxygen2-7.1.2 In-Line Documentation for R
• rpart-4.1-15 Recursive Partitioning and Regression Trees
• rprojroot-2.0.2 Finding Files in Project Subdirectories
• rrcov-1.6-0 Scalable Robust Estimators with High Breakdown Point
• rredlist-0.7.0 ‘IUCN’ Red List Client
• rsample-0.1.1 General Resampling Infrastructure
• rsconnect-0.8.24 Deployment Interface for R Markdown Documents and Shiny Applications
• rslurm-0.6.1 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-0.7.0 Pipe-Friendly Framework for Basic Statistical Tests
• rstudioapi-0.13 Safely Access the RStudio API
• rsvd-1.0.5 Randomized Singular Value Decomposition
• rtracklayer-1.54.0 R interface to genome annotation files and the UCSC genome browser
• ruv-0.9.7.1 Detect and Remove Unwanted Variation using Negative Controls
• rvcheck-0.2.1 R/Package Version Check
• rversions-2.1.1 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
• rvertnet-0.8.2 Search ‘Vertnet’, a ‘Database’ of Vertebrate Specimen Records
• rvest-1.0.2 Easily Harvest (Scrape) Web Pages
• rzmq-0.9.8 R Bindings for ‘ZeroMQ’
• s2-1.0.7 Spherical Geometry Operators Using the S2 Geometry Library
• sampling-2.9 Survey Sampling
• samr-3.0 SAM: Significance Analysis of Microarrays
• sandwich-3.0-1 Robust Covariance Matrix Estimators
• sass-0.4.0 Syntactically Awesome Style Sheets (‘Sass’)
• scales-1.1.1 Scale Functions for Visualization
• scater-1.22.0 Single-Cell Analysis Toolkit for Gene Expression Data in R
• scattermore-0.7 Scatterplots with More Points
• scatterpie-0.1.7 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
• scs-3.0-0 Splitting Conic Solver
• sctransform-0.3.2 Variance Stabilizing Transformations for Single Cell UMI Data
• scuttle-1.4.0 Single-Cell RNA-Seq Analysis Utilities
• seewave-2.1.8 Sound Analysis and Synthesis
• segmented-1.3-4 Regression Models with Break-Points / Change-Points Estimation
• selectr-0.4-2 Translate CSS Selectors to XPath Expressions
• sem-3.1-13 Structural Equation Models
• semPLS-1.0-10 Structural Equation Modeling Using Partial Least Squares
• sendmailR-1.2-1 send email using R
• sensemakr-0.1.4 Sensitivity Analysis Tools for Regression Models
• seqLogo-1.60.0 Sequence logos for DNA sequence alignments
• seqinr-4.2-8 Biological Sequences Retrieval and Analysis
• seqminer-8.2 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-0.23 A Simple HTTP Server to Serve Static Files or Dynamic Documents
• sessioninfo-1.2.0 R Session Information
• setRNG-2013.9-1 Set (Normal) Random Number Generator and Seed
• sets-1.0-19 Sets, Generalized Sets, Customizable Sets and Intervals
• sf-1.0-3 Simple Features for R
• sfsmisc-1.1-12 Utilities from ‘Seminar fuer Statistik’ ETH Zurich
• shadowtext-0.0.9 Shadow Text Grob and Layer
• shape-1.4.6 Functions for Plotting Graphical Shapes, Colors
• shapefiles-0.7 Read and Write ESRI Shapefiles
• shiny-1.7.1 Web Application Framework for R
• shinyBS-0.61 Twitter Bootstrap Components for Shiny
• shinyFiles-0.9.1 A Server-Side File System Viewer for Shiny
• shinycssloaders-1.0.0 Add Loading Animations to a ‘shiny’ Output While It’s Recalculating
• shinydashboard-0.7.2 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-1.2.0 Themes for Shiny
• siggenes-1.68.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
• signal-0.7-7 Signal Processing
• sitmo-2.0.2 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header Files
• slam-0.1-48 Sparse Lightweight Arrays and Matrices
• slider-0.2.2 Sliding Window Functions
• sm-2.2-5.7 Smoothing Methods for Nonparametric Regression and Density Estimation
• smoother-1.1 Functions Relating to the Smoothing of Numerical Data
• sn-2.0.0 The Skew-Normal and Related Distributions Such as the Skew-t and the SUN
• sna-2.6 Tools for Social Network Analysis
• snow-0.4-4 Simple Network of Workstations
• snowfall-1.84-6.1 Easier cluster computing (based on snow).
• snpStats-1.44.0 SnpMatrix and XSnpMatrix classes and methods
• sodium-1.2.0 A Modern and Easy-to-Use Crypto Library
• solrium-1.2.0 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-1.4-5 Classes and Methods for Spatial Data
• spData-2.0.1 Datasets for Spatial Analysis
• spThin-0.2.0 Functions for Spatial Thinning of Species Occurrence Records for Use in Ecological Models
• spaMM-3.9.13 Mixed-Effect Models, with or without Spatial Random Effects
• spaa-0.2.2 SPecies Association Analysis
• spam-2.7-0 SPArse Matrix
• sparklyr-1.7.2 R Interface to Apache Spark
• sparseMatrixStats-1.6.0 Summary Statistics for Rows and Columns of Sparse Matrices
• spatial-7.3-14 Functions for Kriging and Point Pattern Analysis
• spatstat-2.2-0 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
• spatstat.core-2.3-0 Core Functionality of the ‘spatstat’ Family
• spatstat.data-2.1-0 Datasets for ‘spatstat’ Family
• spatstat.geom-2.3-0 Geometrical Functionality of the ‘spatstat’ Family
• spatstat.linnet-2.3-0 Linear Networks Functionality of the ‘spatstat’ Family
• spatstat.sparse-2.0-0 Sparse Three-Dimensional Arrays and Linear Algebra Utilities
• spatstat.utils-2.2-0 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
• spocc-1.2.0 Interface to Species Occurrence Data Sources
• sqldf-0.4-11 Manipulate R Data Frames Using SQL
• squash-1.0.9 Color-Based Plots for Multivariate Visualization
• ssgraph-1.12 Bayesian Graph Structure Learning using Spike-and-Slab Priors
• stabledist-0.7-1 Stable Distribution Functions
• stabs-0.6-4 Stability Selection with Error Control
• stargazer-5.2.2 Well-Formatted Regression and Summary Statistics Tables
• startupmsg-0.9.6 Utilities for Start-Up Messages
• statmod-1.4.36 Statistical Modeling
• statnet-2019.6 Software Tools for the Statistical Analysis of Network Data
• statnet.common-4.5.0 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-0.9.8 Approximate String Matching, Fuzzy Text Search, and String Distance Functions
• stringi-1.7.5 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-1.6.2 Non-Invasive Pretty Printing of R Code
• subplex-1.6 Unconstrained Optimization using the Subplex Algorithm
• survey-4.1-1 Analysis of Complex Survey Samples
• survival-3.2-13 Survival Analysis
• survivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival data
• sva-3.42.0 Surrogate Variable Analysis
• svd-0.5 Interfaces to Various State-of-Art SVD and Eigensolvers
• symmoments-1.2.1 Symbolic Central and Noncentral Moments of the Multivariate Normal Distribution
• sys-3.4 Powerful and Reliable Tools for Running System Commands in R
• systemPipeR-2.0.1 systemPipeR: NGS workflow and report generation environment
• systemfonts-1.0.3 System Native Font Finding
• tableone-0.13.0 Create ‘Table 1’ to Describe Baseline Characteristics with or without Propensity Score Weights
• tables-0.9.6 Formula-Driven Table Generation
• taxize-0.9.99 Taxonomic Information from Around the Web
• tcltk built in
• tcltk2-1.2-11 Tcl/Tk Additions
• 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-4.0.2 Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models
• tergmLite-2.5.5 Fast Simulation of Simple Temporal Exponential Random Graph Models
• terra-1.4-11 Spatial Data Analysis
• testit-0.13 A Simple Package for Testing R Packages
• testthat-3.1.0 Unit Testing for R
• threejs-0.3.3 Interactive 3D Scatter Plots, Networks and Globes
• tibble-3.1.5 Simple Data Frames
• tictoc-1.0.1 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-0.1.4 Easily Install and Load the ‘Tidymodels’ Packages
• tidyposterior-0.1.0 Bayesian Analysis to Compare Models using Resampling Statistics
• tidypredict-0.4.8 Run Predictions Inside the Database
• tidyr-1.1.4 Tidy Messy Data
• tidyselect-1.1.1 Select from a Set of Strings
• tidytext-0.3.2 Text Mining using ‘dplyr’, ‘ggplot2’, and Other Tidy Tools
• tidytree-0.3.6 A Tidy Tool for Phylogenetic Tree Data Manipulation
• tidyverse-1.3.1 Easily Install and Load the ‘Tidyverse’
• tiff-0.1-8 Read and Write TIFF Images
• tilingArray-1.72.0 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-2.0.1 Flexible Regression Models for Survival Data
• tinytex-0.34 Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents
• tkWidgets-1.72.0 R based tk widgets
• tkrplot-0.0-26 TK Rplot
• tm-0.7-8 Text Mining Package
• tmle-1.5.0.2 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-0.2-12 Topic Models
• tree-1.0-41 Classification and Regression Trees
• treeio-1.18.1 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-0.3.4 Tools for Temporal Social Network Analysis
• tsne-0.1-3 T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
• tune-0.1.6 Tidy Tuning Tools
• tuneR-1.3.3.1 Analysis of Music and Speech
• twang-2.5 Toolkit for Weighting and Analysis of Nonequivalent Groups
• tweedie-2.3.3 Evaluation of Tweedie Exponential Family Models
• tweenr-1.0.2 Interpolate Data for Smooth Animations
• tzdb-0.2.0 Time Zone Database Information
• ucminf-1.1-4 General-Purpose Unconstrained Non-Linear Optimization
• udunits2-0.13.1 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-0.7-2 Measurement Units for R Vectors
• unmarked-1.1.1 Models for Data from Unmarked Animals
• 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-2.1.3 Automate Package and Project Setup
• utf8-1.2.2 Unicode Text Processing
• utils built in
• uuid-1.0-2 Tools for Generating and Handling of UUIDs
• uwot-0.1.10 The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction
• vcd-1.4-9 Visualizing Categorical Data
• vcfR-1.12.0 Manipulate and Visualize VCF Data
• vctrs-0.3.8 Vector Helpers
• vegan-2.5-7 Community Ecology Package
• venn-1.10 Draw Venn Diagrams
• vimp-2.2.5 Perform Inference on Algorithm-Agnostic Variable Importance
• vioplot-0.3.7 Violin Plot
• vipor-0.4.5 Plot Categorical Data Using Quasirandom Noise and Density Estimates
• viridis-0.6.2 Colorblind-Friendly Color Maps for R
• viridisLite-0.4.0 Colorblind-Friendly Color Maps (Lite Version)
• visNetwork-2.1.0 Network Visualization using ‘vis.js’ Library
• visdat-0.5.3 Preliminary Visualisation of Data
• vroom-1.5.5 Read and Write Rectangular Text Data Quickly
• vsn-3.62.0 Variance stabilization and calibration for microarray data
• waldo-0.3.1 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-1.1.0 A New Format for Lossless and Lossy Image Compression
• webshot-0.5.2 Take Screenshots of Web Pages
• wellknown-0.7.4 Convert Between ‘WKT’ and ‘GeoJSON’
• whisker-0.4 for R, Logicless Templating
• widgetTools-1.72.0 Creates an interactive tcltk widget
• wikitaxa-0.4.0 Taxonomic Information from ‘Wikipedia’
• withr-2.4.2 Run Code ‘With’ Temporarily Modified Global State
• wk-0.5.0 Lightweight Well-Known Geometry Parsing
• wordcloud-2.6 Word Clouds
• workflows-0.2.4 Modeling Workflows
• workflowsets-0.1.0 Create a Collection of ‘tidymodels’ Workflows
• worrms-0.4.2 World Register of Marine Species (WoRMS) Client
• xCell 1.1.0
• xfun-0.27 Supporting Functions for Packages Maintained by ‘Yihui Xie’
• xgboost-1.4.1.1 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-1.0.5 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
• yaImpute-1.0-32 Nearest Neighbor Observation Imputation and Evaluation Tools
• yaml-2.2.1 Methods to Convert R Data to YAML and Back
• yardstick-0.0.9 Tidy Characterizations of Model Performance
• yulab.utils-0.0.4 Supporting Functions for Packages Maintained by ‘YuLab-SMU’
• 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-2.2.0 Cross-Platform ‘zip’ Compression
• zlibbioc-1.40.0 An R packaged zlib-1.2.5
• zoo-1.8-9 S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations)