Known Issues
Package List
ADGofTest-0.3 Anderson-Darling GoF testAICcmodavg-2.3-1 Model Selection and Multimodel Inference Based on (Q)AIC(c)ALDEx2-1.24.0 Analysis Of Differential Abundance Taking Sample Variation Into AccountALL-1.34.0 A data packageASCAT 2.5.2
AUC-0.3.0 Threshold independent performance measures for probabilistic<U+000a>classifiers.AgiMicroRna-2.42.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAlgDesign-1.2.0 Algorithmic Experimental DesignAnalyzeFMRI-1.1-23 Functions for Analysis of fMRI Datasets Stored in the ANALYZE or
NIFTI FormatAnnotationDbi-1.54.1 Manipulation of SQLite-based annotations in BioconductorAnnotationFilter-1.16.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.34.0 Tools for building SQLite-based annotation data packagesAnnotationHub-3.0.0 Client to access AnnotationHub resourcesArchR 1.0.1
BB-2019.10-1 Solving and Optimizing Large-Scale Nonlinear SystemsBBmisc-1.11 Miscellaneous Helper Functions for B. BischlBCEE-1.3.0 The Bayesian Causal Effect Estimation AlgorithmBDgraph-2.64 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMCBH-1.75.0-0 Boost C++ Header FilesBIGL-1.6.2 Biochemically Intuitive Generalized Loewe ModelBMA-3.18.14 Bayesian Model AveragingBSgenome-1.60.0 Software infrastructure for efficient representation of full genomes and their SNPsBSgenome.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 RBayesPen-1.0 Bayesian Penalized Credible RegionsBayesianTools-0.1.7 General-Purpose MCMC and SMC Samplers and Tools for Bayesian
StatisticsBhat-0.9-10 General likelihood explorationBiasedUrn-1.07 Biased Urn Model DistributionsBiobase-2.52.0 Biobase: Base functions for BioconductorBiocFileCache-2.0.0 Manage Files Across SessionsBiocGenerics-0.38.0 S4 generic functions used in BioconductorBiocIO-1.2.0 Standard Input and Output for Bioconductor PackagesBiocManager-1.30.15 Access the Bioconductor Project Package RepositoryBiocParallel-1.26.0 Bioconductor facilities for parallel evaluationBiocSingular-1.8.1 Singular Value Decomposition for Bioconductor PackagesBiocStyle-2.20.0 Standard styles for vignettes and other Bioconductor documentsBiocVersion-3.13.1 Set the appropriate version of Bioconductor packagesBiostrings-2.60.1 Efficient manipulation of biological stringsBivarP-1.0 Estimating the Parameters of Some Bivariate DistributionsBolstad-0.2-41 Functions for Elementary Bayesian InferenceBolstad2-1.0-28 Bolstad functionsBoruta-7.0.0 Wrapper Algorithm for All Relevant Feature SelectionBradleyTerry2-1.1-2 Bradley-Terry ModelsBrobdingnag-1.2-6 Very Large Numbers in RCGHbase-1.52.0 CGHbase: Base functions and classes for arrayCGH data analysis.CLONETv2-2.1.0 Clonality Estimates in TumorCMA-1.50.0 Synthesis of microarray-based classificationCNEr-1.28.0 CNE Detection and VisualizationCOMPASS-1.30.0 Combinatorial Polyfunctionality Analysis of Single CellsCVST-0.2-2 Fast Cross-Validation via Sequential TestingCairo-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) OutputCategory-2.58.0 Category AnalysisChIPpeakAnno-3.26.0 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome rangesChIPseeker-1.28.3 ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationComICS-1.0.4 Computational Methods for Immune Cell-Type SubsetsCompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal VariablesComplexHeatmap-2.8.0 Make Complex HeatmapsConsensusClusterPlus-1.56.0 ConsensusClusterPlusCovSel-1.2.1 Model-Free Covariate SelectionCytoML-2.4.0 A GatingML Interface for Cross Platform Cytometry Data SharingDAAG-1.24 Data Analysis and Graphics Data and FunctionsDBI-1.1.1 R Database InterfaceDECIPHER-2.20.0 Tools for curating, analyzing, and manipulating biological sequencesDEGseq-1.46.0 Identify Differentially Expressed Genes from RNA-seq dataDESeq2-1.32.0 Differential gene expression analysis based on the negative binomial distributionDEoptimR-1.0-8 Differential Evolution Optimization in Pure RDHARMa-0.4.1 Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression ModelsDNAcopy-1.66.0 DNA copy number data analysisDO.db-2.9 A set of annotation maps describing the entire Disease OntologyDOSE-3.18.0 Disease Ontology Semantic and Enrichment analysisDOT-0.1 Render and Export DOT Graphs in RDRR-0.0.4 Dimensionality Reduction via RegressionDT-0.18 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-0.18.0 A unified framework for working transparently with on-disk and in-memory array-like datasetsDelayedMatrixStats-1.14.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ ObjectsDeriv-4.1.3 Symbolic DifferentiationDescTools-0.99.41 Tools for Descriptive StatisticsDiagrammeR-1.0.6.1 Graph/Network VisualizationDiceDesign-1.9 Designs of Computer ExperimentsDiffBind-3.2.2 Differential Binding Analysis of ChIP-Seq Peak DataDirichletMultinomial-1.34.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataDiscriMiner-0.1-29 Tools of the Trade for Discriminant AnalysisDistributionUtils-0.6-0 Distribution UtilitiesDynDoc-1.70.0 Dynamic document toolsEBImage-4.34.0 Image processing and analysis toolbox for RENMeval-2.0.0 Automated Tuning and Evaluations of Ecological Niche ModelsEasyABC-1.5 Efficient Approximate Bayesian Computation Sampling SchemesEnvStats-2.4.0 Package for Environmental Statistics, Including US EPA GuidanceEpiModel-2.0.5 Mathematical Modeling of Infectious Disease DynamicsExact-2.1 Unconditional Exact TestFDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probesFME-1.3.6.1 A Flexible Modelling Environment for Inverse Modelling,
Sensitivity, Identifiability and Monte Carlo AnalysisFNN-1.1.3 Fast Nearest Neighbor Search Algorithms and ApplicationsFactoMineR-2.4 Multivariate Exploratory Data Analysis and Data MiningFlowSOM-2.0.0 Using self-organizing maps for visualization and interpretation of cytometry dataFormula-1.2-4 Extended Model FormulasGENESIS-2.22.1 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessGEOquery-2.60.0 Get data from NCBI Gene Expression Omnibus (GEO)GGally-2.1.1 Extension to ‘ggplot2’GO.db-3.13.0 A set of annotation maps describing the entire Gene OntologyGOSemSim-2.18.0 GO-terms Semantic Similarity MeasuresGOstats-2.58.0 Tools for manipulating GO and microarraysGPfit-1.0-8 Gaussian Processes ModelingGSA-1.03.1 Gene Set AnalysisGSEABase-1.54.0 Gene set enrichment data structures and methodsGSVA-1.40.1 Gene Set Variation Analysis for microarray and RNA-seq dataGUTS-1.1.1 Fast Calculation of the Likelihood of a Stochastic Survival
ModelGWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association StudiesGWASTools-1.38.0 Tools for Genome Wide Association StudiesGenSA-1.1.7 Generalized Simulated AnnealingGeneNet-1.2.15 Modeling and Inferring Gene NetworksGenomeGraphs 1.46.0
GenomeInfoDb-1.28.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming styleGenomeInfoDbData-1.2.6 Species and taxonomy ID look up tables used by GenomeInfoDbGenomicAlignments-1.28.0 Representation and manipulation of short genomic alignmentsGenomicFeatures-1.44.0 Conveniently import and query gene modelsGenomicFiles-1.28.0 Distributed computing by file or by rangeGenomicRanges-1.44.0 Representation and manipulation of genomic intervalsGetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable InterpolationGillespieSSA-0.6.1 Gillespie’s Stochastic Simulation Algorithm (SSA)Glimma-2.2.0 Interactive HTML graphicsGlobalOptions-0.1.2 Generate Functions to Get or Set Global OptionsGmisc-2.0.2 Descriptive Statistics, Transition Plots, and MoreGreyListChIP-1.24.0 Grey Lists – Mask Artefact Regions Based on ChIP InputsGviz-1.36.1 Plotting data and annotation information along genomic coordinatesHDF5Array-1.20.0 HDF5 backend for DelayedArray objectsHMMcopy-1.34.0 Copy number prediction with correction for GC and mappability bias for HTS dataHSMMSingleCell-1.12.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)HWxtest-1.1.9 Exact Tests for Hardy-Weinberg ProportionsHaploSim-1.8.4 Functions to simulate haplotypesHiddenMarkov-1.8-13 Hidden Markov ModelsHmisc-4.5-0 Harrell MiscellaneousHomo.sapiens-1.3.1 Annotation package for the Homo.sapiens objectIDPmisc-1.1.20 ‘Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)’IHW-1.20.0 Independent Hypothesis WeightingIRanges-2.26.0 Foundation of integer range manipulation in BioconductorIRdisplay-1.0 ‘Jupyter’ Display MachineryISOcodes-2021.02.24 Selected ISO CodesIlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arraysInteractionSet-1.20.0 Base Classes for Storing Genomic Interaction DataIso-0.0-18.1 Functions to Perform Isotonic RegressionJADE-2.0-3 Blind Source Separation Methods Based on Joint Diagonalization
and Some BSS Performance CriteriaJBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J.
ButtlarKEGG.db 3.2.4
KEGGREST-1.32.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)KEGGgraph-1.52.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorKEGGprofile-1.32.0 An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathwayKODAMA-1.6 Knowledge Discovery by Accuracy MaximizationKernSmooth-2.23-20 Functions for Kernel Smoothing Supporting Wand & Jones (1995)LaplacesDemon-16.1.4 Complete Environment for Bayesian InferenceLearnBayes-2.15.1 Functions for Learning Bayesian InferenceLmoments-1.3-1 L-Moments and Quantile MixturesLogicReg-1.6.2 Logic RegressionLymphoSeq-1.20.0 Analyze high-throughput sequencing of T and B cell receptorsLymphoSeqDB-0.99.2 LymphoSeq annotation databasesMAGeCKFlute-1.12.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic ScreensMALDIquant-1.19.3 Quantitative Analysis of Mass Spectrometry DataMASS-7.3-54 Support Functions and Datasets for Venables and Ripley’s MASSMAST-1.18.0 Model-based Analysis of Single Cell TranscriptomicsMCMCglmm-2.32 MCMC Generalised Linear Mixed ModelsMCMCpack-1.5-0 Markov Chain Monte Carlo (MCMC) PackageMIIVsem-0.5.5 Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation ModelsMPV-1.57 Data Sets from Montgomery, Peck and ViningMatchIt-4.1.0 Nonparametric Preprocessing for Parametric Causal InferenceMatching-4.9-9 Multivariate and Propensity Score Matching with Balance
OptimizationMatrix-1.3-3 Sparse and Dense Matrix Classes and MethodsMatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
OperationsMatrixGenerics-1.4.0 S4 Generic Summary Statistic Functions that Operate on Matrix-Like ObjectsMatrixModels-0.5-0 Modelling with Sparse and Dense MatricesMfuzz-2.52.0 Soft clustering of time series gene expression dataModelMetrics-1.2.2.2 Rapid Calculation of Model MetricsNADA-1.6-1.1 Nondetects and Data Analysis for Environmental DataNCmisc-1.1.6 Miscellaneous Functions for Creating Adaptive Functions and
ScriptsNISTunits-1.0.1 Fundamental Physical Constants and Unit Conversions from NISTNLP-0.2-1 Natural Language Processing InfrastructureNOISeq-2.36.0 Exploratory analysis and differential expression for RNA-seq dataOrganismDbi-1.34.0 Software to enable the smooth interfacing of different database packagesPBSddesolve-1.12.6 Solver for Delay Differential EquationsPFAM.db-3.13.0 A set of protein ID mappings for PFAMPICS-2.36.0 Probabilistic inference of ChIP-seqParamHelpers-1.14 Helpers for Parameters in Black-Box Optimization, Tuning and
Machine LearningPermAlgo-1.1 Permutational Algorithm to Simulate Survival DataPoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log
linear modelPolynomF-2.0-3 Polynomials in RPresenceAbsence-1.1.9 Presence-Absence Model Evaluation.ProtGenerics-1.24.0 Generic infrastructure for Bioconductor mass spectrometry packagesQUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix EstimationR.cache-0.15.0 Fast and Light-Weight Caching (Memoization) of Objects and
Results to Speed Up ComputationsR.matlab-3.6.2 Read and Write MAT Files and Call MATLAB from Within RR.methodsS3-1.8.1 S3 Methods SimplifiedR.oo-1.24.0 R Object-Oriented Programming with or without ReferencesR.rsp-0.44.0 Dynamic Generation of Scientific ReportsR.utils-2.10.1 Various Programming UtilitiesR2WinBUGS-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 SemanticsRANN-2.6.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
MetricRBGL-1.68.0 An interface to the BOOST graph libraryRCAL-2.0 Regularized Calibrated EstimationRCircos-1.2.1 Circos 2D Track PlotRColorBrewer-1.1-2 ColorBrewer PalettesRCurl-1.98-1.3 General Network (HTTP/FTP/…) Client Interface for RREDCapR-0.11.0 Interaction Between R and REDCapRGCCA-2.1.2 Regularized and Sparse Generalized Canonical Correlation
Analysis for Multiblock DataRInside-0.2.16 C++ Classes to Embed R in C++ (and C) ApplicationsRItools-0.1-17 Randomization Inference ToolsRJSONIO-1.3-1.4 Serialize R Objects to JSON, JavaScript Object NotationRLRsim-3.1-6 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
ModelsRMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix<U+000a>TheoryRNASeqPower-1.32.0 Sample size for RNAseq studiesRNeXML-2.4.5 Semantically Rich I/O for the ‘NeXML’ FormatRNifti-1.3.1 Fast R and C++ Access to NIfTI ImagesROCR-1.0-11 Visualizing the Performance of Scoring ClassifiersROI-1.0-0 R Optimization InfrastructureROI.plugin.glpk-1.0-0 ‘ROI’ Plug-in ‘GLPK’RPMM-1.25 Recursively Partitioned Mixture ModelRPostgreSQL-0.6-2 R Interface to the ‘PostgreSQL’ Database SystemRPresto-1.3.6 DBI Connector to PrestoRProtoBuf-0.4.17 R Interface to the ‘Protocol Buffers’ ‘API’ (Version 2 or 3)RProtoBufLib-2.4.0 C++ headers and static libraries of Protocol buffersRSNNS-0.4-12 Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)RSQLite-2.2.7 ‘SQLite’ Interface for RRSclient-0.7-3 Client for RserveRSpectra-0.16-0 Solvers for Large-Scale Eigenvalue and SVD ProblemsRUnit-0.4.32 R Unit Test FrameworkRWeka-0.4-43 R/Weka InterfaceRWekajars-3.9.3-2 R/Weka Interface JarsRborist-0.2-3 Extensible, Parallelizable Implementation of the Random Forest
AlgorithmRcpp-1.0.6 Seamless R and C++ IntegrationRcppAnnoy-0.0.18 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
NeighborsRcppArmadillo-0.10.4.0.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra
LibraryRcppCCTZ-0.2.9 ‘Rcpp’ Bindings for the ‘CCTZ’ LibraryRcppDate-0.0.3 ‘date’ C++ Header Library for Date and Time FunctionalityRcppEigen-0.3.3.9.1 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra
LibraryRcppGSL-0.3.8 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and MatricesRcppNumerical-0.4-0 ‘Rcpp’ Integration for Numerical Computing LibrariesRcppParallel-5.1.4 Parallel Programming Tools for ‘Rcpp’RcppProgress-0.4.2 An Interruptible Progress Bar with OpenMP Support for C++ in R
PackagesRcppRoll-0.3.0 Efficient Rolling / Windowed OperationsRcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG
ImplementationsRdpack-2.1.1 Update and Manipulate Rd Documentation ObjectsRdsdp-1.0.5 R Interface to DSDP Semidefinite Programming LibraryRefFreeEWAS-2.2 EWAS using Reference-Free DNA Methylation Mixture DeconvolutionReportingTools-2.32.0 Tools for making reports in various formatsRfast-2.0.3 A Collection of Efficient and Extremely Fast R FunctionsRglpk-0.6-4 R/GNU Linear Programming Kit InterfaceRgraphviz-2.36.0 Provides plotting capabilities for R graph objectsRhdf5lib-1.14.1 hdf5 library as an R packageRhpc-0.19-276 Permits *apply() Style Dispatch for ‘HPC’Rhtslib-1.24.0 HTSlib high-throughput sequencing library as an R packageRingo-1.56.0 R Investigation of ChIP-chip OligoarraysRlabkey-2.7.0 Data Exchange Between R and ‘LabKey’ ServerRmpi-0.6-9.1 Interface (Wrapper) to MPI (Message-Passing Interface)Rook-1.1-1 Rook - a web server interface for RRsamtools-2.8.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importRserve-1.7-3.1 Binary R serverRssa-1.0.3 A Collection of Methods for Singular Spectrum AnalysisRsubread-2.6.1 Mapping, quantification and variant analysis of sequencing dataRtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
ImplementationRttf2pt1-1.3.8 ‘ttf2pt1’ ProgramS4Vectors-0.30.0 Foundation of vector-like and list-like containers in BioconductorSDMTools-1.1-221.2 Species Distribution Modelling Tools: Tools for processing data
associated with species distribution modelling exercisesSKAT-2.0.1 SNP-Set (Sequence) Kernel Association TestSNPRelate-1.26.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)SNPassoc-2.0-2 SNPs-Based Whole Genome Association StudiesSOAR-0.99-11 Memory management in R by delayed assignmentsSPAtest-3.1.2 Score Test and Meta-Analysis Based on Saddlepoint ApproximationSPIA-2.44.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsSQUAREM-2021.1 Squared Extrapolation Methods for Accelerating EM-Like Monotone
AlgorithmsScaledMatrix-1.0.0 Creating a DelayedMatrix of Scaled and Centered ValuesSemiPar-1.0-4.2 Semiparametic RegressionSeqArray-1.32.0 Data management of large-scale whole-genome sequence variant callsSeqVarTools-1.30.0 Tools for variant dataShortRead-1.50.0 FASTQ input and manipulationSignifReg-3.0 Consistent Significance Controlled Variable Selection in
Generalized Linear RegressionSimSeq-1.4.0 Nonparametric Simulation of RNA-Seq DataSingleCellExperiment-1.14.1 S4 Classes for Single Cell DataSnowballC-0.7.0 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 LibrarySparseM-1.81 Sparse Linear AlgebraStanHeaders-2.21.0-7 C++ Header Files for StanSummarizedExperiment-1.22.0 SummarizedExperiment containerSuperLearner-2.0-28 Super Learner PredictionSuppDists-1.1-9.5 Supplementary DistributionsTFBSTools-1.30.0 Software Package for Transcription Factor Binding Site (TFBS) AnalysisTFMPvalue-0.0.8 Efficient and Accurate P-Value Computation for Position Weight
MatricesTFisher-0.2.0 Optimal Thresholding Fisher’s P-Value Combination MethodTH.data-1.0-10 TH’s Data ArchiveTMB-1.7.20 Template Model Builder: A General Random Effect Tool Inspired by
‘ADMB’TTR-0.24.2 Technical Trading RulesTeachingDemos-2.12 Demonstrations for Teaching and LearningTitanCNA-1.30.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumoursTraMineR-2.2-1 Trajectory Miner: a Toolbox for Exploring and Rendering
SequencesTxDb.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 SetsV8-3.4.2 Embedded JavaScript and WebAssembly Engine for RVGAM-1.1-5 Vector Generalized Linear and Additive ModelsVIM-6.1.0 Visualization and Imputation of Missing ValuesVSURF-1.1.0 Variable Selection Using Random ForestsVariantAnnotation-1.38.0 Annotation of Genetic VariantsVennDiagram-1.6.20 Generate High-Resolution Venn and Euler PlotsWeightSVM-1.7-5 Subject Weighted Support Vector MachinesWikidataR-1.4.0 Read-Write API Client Library for ‘Wikidata’WikipediR-1.5.0 A MediaWiki API WrapperWrench-1.10.0 Wrench normalization for sparse count dataWriteXLS-6.3.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) FilesXML-3.99-0.6 Tools for Parsing and Generating XML Within R and S-PlusXVector-0.32.0 Foundation of external vector representation and manipulation in Bioconductorabc-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 Eliminationabind-1.4-5 Combine Multidimensional Arraysacepack-1.4.1 ACE and AVAS for Selecting Multiple Regression Transformationsadabag-4.2 Applies Multiclass AdaBoost.M1, SAMME and Baggingade4-1.7-16 Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciencesadmisc-0.15 Adrian Dusa’s Miscellaneousaffxparser-1.64.0 Affymetrix File Parsing SDKaffy-1.70.0 Methods for Affymetrix Oligonucleotide Arraysaffycoretools-1.64.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChipsaffyio-1.62.0 Tools for parsing Affymetrix data filesaggregation-1.0.1 p-Value Aggregation Methodsakima-0.6-2.1 Interpolation of Irregularly and Regularly Spaced Dataalr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Editionamap-0.8-18 Another Multidimensional Analysis Packageanimation-2.6 A Gallery of Animations in Statistics and Utilities to Create
Animationsannaffy-1.63.1 Annotation tools for Affymetrix biological metadataannotate-1.70.0 Annotation for microarraysaod-1.3.1 Analysis of Overdispersed Dataape-5.5 Analyses of Phylogenetics and Evolutionapeglm-1.14.0 Approximate posterior estimation for GLM coefficientsaplot-0.0.6 Decorate a ‘ggplot’ with Associated Informationargparse-2.0.3 Command Line Optional and Positional Argument Parserargparser-0.7.1 Command-Line Argument Parserarm-1.11-2 Data Analysis Using Regression and Multilevel/Hierarchical
Modelsarsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical
Summariesarules-1.6-8 Mining Association Rules and Frequent Itemsetsash-1.0-15 David Scott’s ASH Routinesashr-2.2-47 Methods for Adaptive Shrinkage, using Empirical Bayesaskpass-1.1 Safe Password Entry for R, Git, and SSHasnipe-1.1.15 Animal Social Network Inference and Permutations for Ecologistsassertive-0.3-6 Readable Check Functions to Ensure Code Integrityassertive.base-0.0-9 A Lightweight Core of the ‘assertive’ Packageassertive.code-0.0-3 Assertions to Check Properties of Codeassertive.data-0.0-3 Assertions to Check Properties of Dataassertive.data.uk-0.0-2 Assertions to Check Properties of Stringsassertive.data.us-0.0-2 Assertions to Check Properties of Stringsassertive.datetimes-0.0-3 Assertions to Check Properties of Dates and Timesassertive.files-0.0-2 Assertions to Check Properties of Filesassertive.matrices-0.0-2 Assertions to Check Properties of Matricesassertive.models-0.0-2 Assertions to Check Properties of Modelsassertive.numbers-0.0-2 Assertions to Check Properties of Numbersassertive.properties-0.0-4 Assertions to Check Properties of Variablesassertive.reflection-0.0-5 Assertions for Checking the State of Rassertive.sets-0.0-3 Assertions to Check Properties of Setsassertive.strings-0.0-3 Assertions to Check Properties of Stringsassertive.types-0.0-3 Assertions to Check Types of Variablesassertthat-0.2.1 Easy Pre and Post Assertionsaudio-0.1-7 Audio Interface for Raws-2.5-1 Adaptive Weights Smoothingaws.ec2metadata-0.2.0 Get EC2 Instance Metadataaws.s3-0.3.21 ‘AWS S3’ Client Packageaws.signature-0.6.0 Amazon Web Services Request SignaturesawsMethods-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 Formatbackports-1.2.1 Reimplementations of Functions Introduced Since R-3.0.0bacr-1.0.1 Bayesian Adjustment for Confoundingbamsignals-1.24.0 Extract read count signals from bam filesbartMachine-1.2.6 Bayesian Additive Regression TreesbartMachineJARs-1.1 bartMachine JARsbase built in
base64-2.0 Base64 Encoder and Decoderbase64enc-0.1-3 Tools for base64 encodingbase64url-1.4 Fast and URL-Safe Base64 Encoder and Decoderbatchmeans-1.0-4 Consistent Batch Means Estimation of Monte Carlo Standard Errorsbatchtools-0.9.15 Tools for Computation on Batch SystemsbaySeq-2.26.0 Empirical Bayesian analysis of patterns of differential expression in count databayesm-3.1-4 Bayesian Inference for Marketing/Micro-Econometricsbayesplot-1.8.0 Plotting for Bayesian Modelsbbmle-1.0.23.1 Tools for General Maximum Likelihood Estimationbdsmatrix-1.3-4 Routines for Block Diagonal Symmetric Matricesbeachmat-2.8.0 Compiling Bioconductor to Handle Each Matrix Typebeanplot-1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin<U+000a>Plot)beeswarm-0.3.1 The Bee Swarm Plot, an Alternative to Stripchartbenchmark-0.3-6 Benchmark Experiments Toolboxbetareg-3.1-4 Beta Regressionbezier-1.1.2 Toolkit for Bezier Curves and Splinesbibtex-0.4.2.3 Bibtex Parserbiglm-0.9-2.1 Bounded Memory Linear and Generalized Linear Modelsbigmemory-4.5.36 Manage Massive Matrices with Shared Memory and Memory-Mapped
Filesbigmemory.sri-0.1.3 A shared resource interface for Bigmemory Project packagesbindr-0.1.1 Parametrized Active Bindingsbindrcpp-0.2.2 An ‘Rcpp’ Interface to Active Bindingsbio3d-2.4-2 Biological Structure Analysisbiom-0.3.12 An interface package (beta) for the BIOM file format.biomaRt-2.48.0 Interface to BioMart databases (i.e. Ensembl)biomformat-1.20.0 An interface package for the BIOM file formatbiovizBase-1.40.0 Basic graphic utilities for visualization of genomic data.bit-4.0.4 Classes and Methods for Fast Memory-Efficient Boolean Selectionsbit64-4.0.5 A S3 Class for Vectors of 64bit Integersbitops-1.0-7 Bitwise Operationsblavaan-0.3-15 Bayesian Latent Variable Analysisblob-1.2.1 A Simple S3 Class for Representing Vectors of Binary Data
(‘BLOBS’)bmp-0.3 Read Windows Bitmap (BMP) Imagesbnlearn-4.6.1 Bayesian Network Structure Learning, Parameter Learning and
Inferencebold-1.2.0 Interface to Bold Systems APIbookdown-0.22 Authoring Books and Technical Documents with R Markdownboot-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 Modelingbrew-1.0-6 Templating Framework for Report Generationbrglm-0.7.2 Bias Reduction in Binomial-Response Generalized Linear Modelsbridgedist-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 Factorsbrio-1.1.2 Basic R Input Outputbrms-2.15.0 Bayesian Regression Models using ‘Stan’broom-0.7.6 Convert Statistical Objects into Tidy Tibblesbslib-0.2.5.1 Custom ‘Bootstrap’ ‘Sass’ Themes for ‘shiny’ and ‘rmarkdown’bst-0.3-23 Gradient Boostingbumphunter-1.34.0 Bump HuntercaTools-1.18.2 Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etccachem-1.0.5 Cache R Objects with Automatic Pruningcalibrate-1.7.7 Calibration of Scatterplot and Biplot Axescallr-3.7.0 Call R from Rcar-3.0-10 Companion to Applied RegressioncarData-3.0-4 Companion to Applied Regression Data Setscaret-6.0-88 Classification and Regression Trainingcatdata-1.2.2 Categorical Datacelestial-1.4.6 Collection of Common Astronomical Conversion Routines and
Functionscellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columnscgdsr-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 Checkschemometrics-1.4.2 Multivariate Statistical Analysis in Chemometricschipseq-1.42.0 chipseq: A package for analyzing chipseq datachromVAR-1.14.0 Chromatin Variation Across Regionschron-2.3-56 Chronological Objects which can Handle Dates and Timescirclize-0.4.12 Circular Visualizationcircular-0.4-93 Circular StatisticsclValid-0.7 Validation of Clustering Resultsclass-7.3-19 Functions for ClassificationclassInt-0.4-3 Choose Univariate Class Intervalscli-2.5.0 Helpers for Developing Command Line Interfacesclipr-0.7.1 Read and Write from the System Clipboardclisymbols-1.2.0 Unicode Symbols at the R Promptclue-0.3-59 Cluster Ensemblescluster-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-4.0.0 statistical analysis and visualization of functional profiles for genes and gene clustersclusterRepro-0.9 Reproducibility of Gene Expression Clustersclustree-0.4.3 Visualise Clusterings at Different Resolutionscobs-1.3-4 Constrained B-Splines (Sparse Matrix Based)coda-0.19-4 Output Analysis and Diagnostics for MCMCcodetools-0.2-18 Code Analysis Tools for Rcoin-1.4-1 Conditional Inference Procedures in a Permutation Test FrameworkcolorRamps-2.3 Builds color tablescolorspace-2.0-1 A Toolbox for Manipulating and Assessing Colors and Palettescolourpicker-1.1.0 A Colour Picker Tool for Shiny and for Selecting Colours in
Plotscombinat-0.0-8 combinatorics utilitiescommonmark-1.7 High Performance CommonMark and Github Markdown Rendering in Rcompare-0.2-6 Comparing Objects for Differencescompositions-2.0-1 Compositional Data Analysisconditionz-0.1.0 Control How Many Times Conditions are Thrownconfig-0.3.1 Manage Environment Specific Configuration Valuesconflicted-1.0.4 An Alternative Conflict Resolution Strategyconquer-1.0.2 Convolution-Type Smoothed Quantile RegressioncopCAR-2.0-4 Fitting the copCAR Regression Model for Discrete Areal Datacopula-1.0-1 Multivariate Dependence with Copulascopynumber-1.32.0 Segmentation of single- and multi-track copy number data by penalized least squares regression.corpcor-1.6.9 Efficient Estimation of Covariance and (Partial) Correlationcorrplot-0.88 Visualization of a Correlation Matrixcovr-3.5.1 Test Coverage for Packagescowplot-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 Modelcoxme-2.2-16 Mixed Effects Cox Modelscpp11-0.2.7 A C++11 Interface for R’s C Interfacecrayon-1.4.1 Colored Terminal Outputcredentials-1.3.0 Tools for Managing SSH and Git Credentialscrosstalk-1.1.1 Inter-Widget Interactivity for HTML Widgetscrul-1.1.0 HTTP ClientcsSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarraysctmle-0.1.2 Collaborative Targeted Maximum Likelihood Estimationcubature-2.0.4.2 Adaptive Multivariate Integration over HypercubescummeRbund-2.34.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.curl-4.3.1 A Modern and Flexible Web Client for Rcurry-0.1.1 Partial Function Application with %<%, %-<%, and %><%cvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervalscyclocomp-1.1.0 Cyclomatic Complexity of R Codecytolib-2.4.0 C++ infrastructure for representing and interacting with the gated cytometry datad3Network-0.5.2.1 Tools for creating D3 JavaScript network, tree, dendrogram, and<U+000a>Sankey graphs from RdHSIC-2.1 Independence Testing via Hilbert Schmidt Independence Criteriondada2-1.20.0 Accurate, high-resolution sample inference from amplicon sequencing datadata.table-1.14.0 Extension of data.framedata.tree-1.0.0 General Purpose Hierarchical Data Structuredatasets built in
dbarts-0.9-19 Discrete Bayesian Additive Regression Trees Samplerdbplyr-2.1.1 A ‘dplyr’ Back End for Databasesddalpha-1.3.11 Depth-Based Classification and Calculation of Data DepthdeSolve-1.28 Solvers for Initial Value Problems of Differential Equations
(‘ODE’, ‘DAE’, ‘DDE’)deal-1.2-39 Learning Bayesian Networks with Mixed Variablesdebugme-1.1.0 Debug R Packagesdegreenet-1.3-3 Models for Skewed Count Distributions Relevant to Networksdeldir-0.2-10 Delaunay Triangulation and Dirichlet (Voronoi) Tessellationdendextend-1.15.1 Extending ‘dendrogram’ Functionality in Rderfinder-1.26.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approachderfinderHelper-1.26.0 derfinder helper packagedesc-1.3.0 Manipulate DESCRIPTION Filesdescr-1.1.5 Descriptive Statisticsdevtools-2.4.1 Tools to Make Developing R Packages Easierdfidx-0.0-4 Indexed Data Framesdfoptim-2020.10-1 Derivative-Free Optimizationdiagram-1.6.5 Functions for Visualising Simple Graphs (Networks), Plotting
Flow Diagramsdials-0.0.9 Tools for Creating Tuning Parameter Valuesdiamonds-1.0-5 Analysis and sampling grids from diamond partitionsdichromat-2.0-0 Color Schemes for Dichromatsdiffobj-0.3.4 Diffs for R ObjectsdiffusionMap-1.2.0 Diffusion Mapdigest-0.6.27 Create Compact Hash Digests of R ObjectsdimRed-0.2.3 A Framework for Dimensionality Reductiondiptest-0.76-0 Hartigan’s Dip Test Statistic for Unimodality - Correcteddismo-1.3-3 Species Distribution Modelingdistillery-1.2-1 Method Functions for Confidence Intervals and to Distill
Information from an Objectdistr-2.8.0 Object Oriented Implementation of DistributionsdistrEx-2.8.0 Extensions of Package ‘distr’diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis
PackagedoBy-4.6.10 Groupwise Statistics, LSmeans, Linear Contrasts, UtilitiesdoMC-1.3.7 Foreach Parallel Adaptor for ‘parallel’doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi PackagedoParallel-1.0.16 Foreach Parallel Adaptor for the ‘parallel’ PackagedoRNG-1.8.2 Generic Reproducible Parallel Backend for ‘foreach’ LoopsdoSNOW-1.0.19 Foreach Parallel Adaptor for the ‘snow’ PackagedotCall64-1.0-1 Enhanced Foreign Function Interface Supporting Long Vectorsdownloader-0.4 Download Files over HTTP and HTTPSdplyr-1.0.6 A Grammar of Data Manipulationdqrng-0.3.0 Fast Pseudo Random Number Generatorsdr-3.0.10 Methods for Dimension Reduction for Regressiondrgee-1.1.10 Doubly Robust Generalized Estimating EquationsdrugCombo-1.1.1 Drug Interaction Modeling Based on Loewe Additivity Following
Harbron’s Approachdtangle-2.0.9 Cell Type Deconvolution from Gene Expressionsdtplyr-1.1.0 Data Table Back-End for ‘dplyr’dtw-1.22-3 Dynamic Time Warping Algorithmsdummies-1.5.6 Create dummy/indicator variables flexibly and efficientlydygraphs-1.1.1.6 Interface to ‘Dygraphs’ Interactive Time Series Charting LibrarydynamicTreeCut-1.63-1 Methods for Detection of Clusters in Hierarchical Clustering
Dendrogramse1071-1.7-6 Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wienearth-5.3.0 Multivariate Adaptive Regression SplinesedgeR-3.34.0 Empirical Analysis of Digital Gene Expression Data in Relasticnet-1.3 Elastic-Net for Sparse Estimation and Sparse PCAelementR-1.3.7 An Framework for Reducing Elemental LAICPMS Data from Solid
Structuresellipse-0.4.2 Functions for Drawing Ellipses and Ellipse-Like Confidence
Regionsellipsis-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 Programsenergy-1.7-8 E-Statistics: Multivariate Inference via the Energy of Dataenrichplot-1.12.0 Visualization of Functional Enrichment Resultensembldb-2.16.0 Utilities to create and use Ensembl-based annotation databasesentropy-1.3.0 Estimation of Entropy, Mutual Information and Related Quantitiesepitools-0.5-10.1 Epidemiology Toolsergm-3.11.0 Fit, Simulate and Diagnose Exponential-Family Models for
Networksergm.count-3.4.0 Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edgesetrunct-0.1 Computes Moments of Univariate Truncated t Distributioneuropepmc-0.4 R Interface to the Europe PubMed Central RESTful Web Serviceevaluate-0.14 Parsing and Evaluation Tools that Provide More Details than the
Defaultexpm-0.999-6 Matrix Exponential, Log, ‘etc’expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”extRemes-2.1 Extreme Value Analysisextrafont-0.17 Tools for using fontsextrafontdb-1.0 Package for holding the database for the extrafont packagefANCOVA-0.6-1 Nonparametric Analysis of Covariancefail-1.3 File Abstraction Interface Layer (FAIL)fansi-0.4.2 ANSI Control Sequence Aware String Functionsfaraway-1.0.7 Functions and Datasets for Books by Julian Farawayfarver-2.1.0 High Performance Colour Space ManipulationfastICA-1.2-2 FastICA Algorithms to Perform ICA and Projection Pursuitfastcluster-1.1.25 Fast Hierarchical Clustering Routines for R and ‘Python’fasterize-1.0.3 Fast Polygon to Raster Conversionfastmap-1.1.0 Fast Data Structuresfastmatch-1.1-0 Fast match() functionfastseg-1.38.0 fastseg - a fast segmentation algorithmfasttime-1.0-2 Fast Utility Function for Time Parsing and Conversionfda-5.1.9 Functional Data Analysisfdrtool-1.2.16 Estimation of (Local) False Discovery Rates and Higher Criticismfds-1.8 Functional Data Setsfeather-0.3.5 R Bindings to the Feather ‘API’ff-4.0.4 Memory-Efficient Storage of Large Data on Disk and Fast Access
Functionsffbase-0.13.3 Basic Statistical Functions for Package ‘ff’fftw-1.0-6 Fast FFT and DCT Based on the FFTW Libraryfftwtools-0.9-11 Wrapper for ‘FFTW3’ Includes: One-Dimensional, Two-Dimensional,
Three-Dimensional, and Multivariate Transformsfgsea-1.18.0 Fast Gene Set Enrichment Analysisfields-12.3 Tools for Spatial Datafilehash-2.4-2 Simple Key-Value Databasefilelock-1.0.2 Portable File Lockingfindpython-1.0.7 Functions to Find an Acceptable Python BinaryfishMod-0.29 Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta
Log-Normal Modelsfit.models-0.64 Compare Fitted Modelsfitdistrplus-1.1-3 Help to Fit of a Parametric Distribution to Non-Censored or
Censored DataflashClust-1.01-2 Implementation of optimal hierarchical clusteringflexclust-1.4-0 Flexible Cluster Algorithmsflexmix-2.3-17 Flexible Mixture ModelingflowClust-3.30.0 Clustering for Flow CytometryflowCore-2.4.0 flowCore: Basic structures for flow cytometry dataflowStats-4.4.0 Statistical methods for the analysis of flow cytometry dataflowViz-1.56.0 Visualization for flow cytometryflowWorkspace-4.4.0 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 Experimentsforcats-0.5.1 Tools for Working with Categorical Variables (Factors)foreach-1.5.1 Provides Foreach Looping Constructforecast-8.14 Forecasting Functions for Time Series and Linear Modelsforeign-0.8-81 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’,
‘Systat’, ‘Weka’, ‘dBase’, …forestplot-1.10.1 Advanced Forest Plot Using ‘grid’ Graphicsforge-0.2.0 Casting Values into ShapeformatR-1.9 Format R Code Automaticallyformula.tools-1.7.1 Programmatic Utilities for Manipulating Formulas, Expressions,
Calls, Assignments and Other R Objectsfossil-0.4.0 Palaeoecological and Palaeogeographical Analysis Toolsfpc-2.2-9 Flexible Procedures for Clusteringfpp-0.5 Data for “Forecasting: principles and practice”fracdiff-1.5-1 Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Modelsfs-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-0.2.2 Apply Mapping Functions in Parallel using Futuresfutile.logger-1.4.3 A Logging Utility for Rfutile.options-1.0.1 Futile Options Managementfuture-1.21.0 Unified Parallel and Distributed Processing in R for Everyonefuture.apply-1.7.0 Apply Function to Elements in Parallel using FuturesgWidgets2-1.0-8 Rewrite of gWidgets API for Simplified GUI ConstructiongWidgets2tcltk-1.0-6 Toolkit Implementation of gWidgets2 for tcltkgage-2.42.0 Generally Applicable Gene-set Enrichment for Pathway Analysisgam-1.20 Generalized Additive Modelsgamlss-5.3-4 Generalised Additive Models for Location Scale and Shapegamlss.data-6.0-1 Data for Generalised Additive Models for Location Scale and
Shapegamlss.dist-5.3-2 Distributions for Generalized Additive Models for Location Scale
and Shapegamlss.tr-5.1-7 Generating and Fitting Truncated `gamlss.family’ Distributionsgamm4-0.2-6 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’gap-1.2.3-1 Genetic Analysis Packagegapfill-0.9.6-1 Fill Missing Values in Satellite Datagargle-1.1.0 Utilities for Working with Google APIsgaussquad-1.0-2 Collection of functions for Gaussian quadraturegbRd-0.4-11 Utilities for processing Rd objects and filesgbm-2.1.8 Generalized Boosted Regression Modelsgclus-1.3.2 Clustering Graphicsgcrma-2.64.0 Background Adjustment Using Sequence Informationgdata-2.18.0 Various R Programming Tools for Data Manipulationgdistance-1.3-6 Distances and Routes on Geographical Gridsgdsfmt-1.28.0 R Interface to CoreArray Genomic Data Structure (GDS) filesgdtools-0.2.3 Utilities for Graphical Renderinggee-4.13-20 Generalized Estimation Equation Solvergeepack-1.3-2 Generalized Estimating Equation Packagegeiger-2.0.7 Analysis of Evolutionary DiversificationgeneLenDataBase-1.28.0 Lengths of mRNA transcripts for a number of genomesgenefilter-1.74.0 genefilter: methods for filtering genes from high-throughput experimentsgeneplotter-1.70.0 Graphics related functions for Bioconductorgenerics-0.1.0 Common S3 Generics not Provided by Base R Methods Related to
Model Fittinggenoset-1.45.1 A RangedSummarizedExperiment with methods for copy number analysisgeometry-0.4.5 Mesh Generation and Surface Tessellationgert-1.3.0 Simple Git Client for Rgetopt-1.20.3 C-Like ‘getopt’ BehaviorggExtra-0.9 Add Marginal Histograms to ‘ggplot2’, and More ‘ggplot2’
Enhancementsggbeeswarm-0.6.0 Categorical Scatter (Violin Point) Plotsggbio-1.40.0 Visualization tools for genomic dataggcyto-1.20.0 Visualize Cytometry data with ggplotggdendro-0.1.22 Create Dendrograms and Tree Diagrams Using ‘ggplot2’ggfan-0.1.3 Summarise a Distribution Through Coloured Intervalsggforce-0.3.3 Accelerating ‘ggplot2’ggnetwork-0.5.8 Geometries to Plot Networks with ‘ggplot2’ggnewscale-0.4.5 Multiple Fill and Colour Scales in ‘ggplot2’ggplot2-3.3.3 Create Elegant Data Visualisations Using the Grammar of Graphicsggplotify-0.0.7 Convert Plot to ‘grob’ or ‘ggplot’ Objectggpointdensity-0.1.0 A Cross Between a 2D Density Plot and a Scatter Plotggpubr-0.4.0 ‘ggplot2’ Based Publication Ready Plotsggraph-2.0.5 An Implementation of Grammar of Graphics for Graphs and Networksggrepel-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-0.6.1 Significance Brackets for ‘ggplot2’ggthemes-4.2.4 Extra Themes, Scales and Geoms for ‘ggplot2’ggtree-3.0.2 an R package for visualization of tree and annotation dataggvis-0.4.7 Interactive Grammar of Graphicsgh-1.3.0 ‘GitHub’ ‘API’git2r-0.28.0 Provides Access to Git Repositoriesgitcreds-0.1.1 Query ‘git’ Credentials from ‘R’glasso-1.11 Graphical Lasso: Estimation of Gaussian Graphical Modelsgld-2.6.2 Estimation and Use of the Generalised (Tukey) Lambda
Distributiongllvm-1.3.0 Generalized Linear Latent Variable ModelsglmmML-1.1.1 Generalized Linear Models with ClusteringglmmTMB-1.0.2.1 Generalized Linear Mixed Models using Template Model Builderglmnet-4.1-1 Lasso and Elastic-Net Regularized Generalized Linear Modelsglmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox
Proportional Hazards Modelglobals-0.14.0 Identify Global Objects in R Expressionsglue-1.4.2 Interpreted String Literalsgmm-1.6-6 Generalized Method of Moments and Generalized Empirical
Likelihoodgmodels-2.18.1 Various R Programming Tools for Model Fittinggmp-0.6-2 Multiple Precision Arithmeticgnumeric-0.7-8 Read Data from Files Readable by ‘gnumeric’goftest-1.2-2 Classical Goodness-of-Fit Tests for Univariate Distributionsgomms-1.0 GLM-Based Ordination Methodgoogledrive-1.0.1 An Interface to Google Drivegooglesheets4-0.3.0 Access Google Sheets using the Sheets API V4goseq-1.44.0 Gene Ontology analyser for RNA-seq and other length biased datagower-0.2.2 Gower’s Distancegplots-3.1.1 Various R Programming Tools for Plotting DatagrDevices built in
grImport2-0.2-0 Importing ‘SVG’ Graphicsgraph-1.70.0 graph: A package to handle graph data structuresgraphics built in
graphlayouts-0.7.1 Additional Layout Algorithms for Network Visualizationsgrid built in
gridBase-0.4-7 Integration of base and grid graphicsgridExtra-2.3 Miscellaneous Functions for “Grid” GraphicsgridGraphics-0.5-1 Redraw Base Graphics Using ‘grid’ Graphicsgrpreg-3.3.1 Regularization Paths for Regression Models with Grouped
Covariatesgsalib-2.1 Utility Functions For GATKgsl-2.1-6 Wrapper for the Gnu Scientific Librarygsubfn-0.7 Utilities for Strings and Function Argumentsgsw-1.0-5 Gibbs Sea Water Functionsgtable-0.3.0 Arrange ‘Grobs’ in Tablesgtools-3.8.2 Various R Programming Toolsh2o-3.32.1.2 R Interface for the ‘H2O’ Scalable Machine Learning Platformhapassoc-1.2-8 Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithmhaplo.stats-1.8.6 Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguoushardhat-0.1.5 Construct Modeling Packageshaven-2.4.1 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Fileshdf5r-1.3.3 Interface to the ‘HDF5’ Binary Data Formathdm-0.3.1 High-Dimensional Metricshdrcde-3.4 Highest Density Regions and Conditional Density Estimationheatmap3-1.1.9 An Improved Heatmap Packagehexbin-1.28.2 Hexagonal Binning Routineshgu133plus2.db-3.13.0 Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)highr-0.9 Syntax Highlighting for R Source Codehms-1.1.0 Pretty Time of Dayhopach-2.52.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)htmlTable-2.2.1 Advanced Tables for Markdown/HTMLhtmltools-0.5.1.1 Tools for HTMLhtmlwidgets-1.5.3 HTML Widgets for Rhttpcode-0.3.0 ‘HTTP’ Status Code Helperhttpuv-1.6.1 HTTP and WebSocket Server Libraryhttr-1.4.2 Tools for Working with URLs and HTTPhuge-1.3.4.1 High-Dimensional Undirected Graph Estimationhunspell-3.0.1 High-Performance Stemmer, Tokenizer, and Spell Checkerhwriter-1.3.2 HTML Writer - Outputs R objects in HTML formathypergate-0.8.3 Machine Learning of Hyperrectangular Gating Strategies for
High-Dimensional Cytometryica-1.0-2 Independent Component Analysisidr-1.2 Irreproducible discovery rateids-1.0.1 Generate Random Identifiersie2misc-0.8.6 Irucka Embry’s Miscellaneous USGS Functionsigraph-1.2.6 Network Analysis and Visualizationigraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Packageilluminaio-0.34.0 Parsing Illumina Microarray Output Filesimager-0.42.8 Image Processing Library Based on ‘CImg’imagerExtra-1.3.2 Extra Image Processing Library Based on ‘imager’impute-1.66.0 impute: Imputation for microarray dataineq-0.2-13 Measuring Inequality, Concentration, and Povertyinfer-0.5.4 Tidy Statistical Inferenceinferference-1.0.2 Methods for Causal Inference with InterferenceinfluenceR-0.1.0 Software Tools to Quantify Structural Importance of Nodes in a
Networkinfotheo-1.2.0 Information-Theoretic Measuresini-0.3.1 Read and Write ‘.ini’ Filesinline-0.3.18 Functions to Inline C, C++, Fortran Function Calls from RinteractiveDisplayBase-1.30.0 Base package for enabling powerful shiny web displays of Bioconductor objectsintergraph-2.0-2 Coercion Routines for Network Data ObjectsinterpretR-0.2.4 Binary Classifier and Regression Model Interpretation FunctionsintrinsicDimension-1.2.0 Intrinsic Dimension Estimationinum-1.0-4 Interval and Enum-Type Representation of Vectorsinvgamma-1.1 The Inverse Gamma Distributioniotools-0.3-1 I/O Tools for Streamingipred-0.9-11 Improved Predictorsirace-3.4.1 Iterated Racing for Automatic Algorithm Configurationirlba-2.3.3 Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matricesisoband-0.2.4 Generate Isolines and Isobands from Regularly Spaced Elevation
Gridsiterators-1.0.13 Provides Iterator Constructitertools-0.1-3 Iterator Toolsits-1.1.8 Irregular Time Seriesjaneaustenr-0.1.5 Jane Austen’s Complete NovelsjiebaR-0.11 Chinese Text SegmentationjiebaRD-0.1 Chinese Text Segmentation Data for jiebaR Packagejomo-2.7-2 Multilevel Joint Modelling Multiple Imputationjpeg-0.1-8.1 Read and write JPEG imagesjquerylib-0.1.4 Obtain ‘jQuery’ as an HTML Dependency Objectjsonlite-1.7.2 A Simple and Robust JSON Parser and Generator for Rjstable-1.0.2 Create Tables from Different Types of RegressionkaryoploteR-1.18.0 Plot customizable linear genomes displaying arbitrary datakedd-1.0.3 Kernel Estimator and Bandwidth Selection for Density and Its
Derivativeskernlab-0.9-29 Kernel-Based Machine Learning Labkin.cohort-0.7 Analysis of Kin-Cohort Studieskinship2-1.8.5 Pedigree FunctionsklaR-0.6-15 Classification and Visualizationknitr-1.33 A General-Purpose Package for Dynamic Report Generation in Rknockoff-0.3.3 The Knockoff Filter for Controlled Variable Selectionkohonen-3.0.10 Supervised and Unsupervised Self-Organising Mapsks-1.12.0 Kernel Smoothingkyotil-2021.5-14 Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studieslabdsv-2.0-1 Ordination and Multivariate Analysis for Ecologylabeling-0.4.2 Axis Labelinglabelled-2.8.0 Manipulating Labelled Datalaeken-0.5.1 Estimation of Indicators on Social Exclusion and Povertylambda.r-1.2.4 Modeling Data with Functional Programminglars-1.2 Least Angle Regression, Lasso and Forward Stagewiselasso2-1.2-21.1 L1 Constrained Estimation aka `lasso’latentnet-2.10.5 Latent Position and Cluster Models for Statistical Networkslater-1.2.0 Utilities for Scheduling Functions to Execute Later with Event
Loopslattice-0.20-44 Trellis Graphics for RlatticeExtra-0.6-29 Extra Graphical Utilities Based on Latticelava-1.6.9 Latent Variable Modelslavaan-0.6-8 Latent Variable Analysislazy-1.2-16 Lazy Learning for Local Regressionlazyeval-0.2.2 Lazy (Non-Standard) Evaluationlda-1.4.2 Collapsed Gibbs Sampling Methods for Topic Modelsleaps-3.1 Regression Subset Selectionleiden-0.3.7 R Implementation of Leiden Clustering Algorithmlhs-1.1.1 Latin Hypercube Sampleslibcoin-1.0-8 Linear Test Statistics for Permutation Inferencelifecycle-1.0.0 Manage the Life Cycle of your Package FunctionslimSolve-1.5.6 Solving Linear Inverse Modelslimma-3.48.0 Linear Models for Microarray Datalinprog-0.9-2 Linear Programming / Optimizationlintr-2.0.1 A ‘Linter’ for R CodeliquidSVM-1.2.4 A Fast and Versatile SVM Packagelistenv-0.8.0 Environments Behaving (Almost) as Listslme4-1.1-27 Linear Mixed-Effects Models using ‘Eigen’ and S4lmerTest-3.1-3 Tests in Linear Mixed Effects Modelslmom-2.8 L-Momentslmtest-0.9-38 Testing Linear Regression Modelslocfdr-1.1-8 Computes Local False Discovery Rateslocfit-1.5-9.4 Local Regression, Likelihood and Density Estimationlogcondens-2.1.5 Estimate a Log-Concave Probability Density from Iid Observationslogistf-1.24 Firth’s Bias-Reduced Logistic Regressionlogspline-2.1.16 Routines for Logspline Density Estimationlokern-1.1-9 Kernel Regression Smoothing with Local or Global Plug-in
Bandwidthlongitudinal-1.1.12 Analysis of Multiple Time Course Datalongmemo-1.1-2 Statistics for Long-Memory Processes (Book Jan Beran), and
Related Functionalityloo-2.4.1 Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
ModelslpSolve-5.6.15 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programslpridge-1.0-8 Local Polynomial (Ridge) Regressionlpsymphony-1.20.0 Symphony integer linear programming solver in Rlqa-1.0-3 Penalized Likelihood Inference for GLMslsei-1.3-0 Solving Least Squares or Quadratic Programming Problems under
Equality/Inequality Constraintslubridate-1.7.10 Make Dealing with Dates a Little Easierlumi-2.44.0 BeadArray Specific Methods for Illumina Methylation and Expression MicroarraysmRMRe-2.1.0 Parallelized Minimum Redundancy, Maximum Relevance (mRMR)maSigPro-1.64.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Datamagic-1.5-9 Create and Investigate Magic Squaresmagick-2.7.2 Advanced Graphics and Image-Processing in Rmagrittr-2.0.1 A Forward-Pipe Operator for RmanipulateWidget-0.10.1 Add Even More Interactivity to Interactive Chartsmapdata-2.3.0 Extra Map Databasesmapproj-1.2.7 Map Projectionsmaps-3.3.0 Draw Geographical Mapsmaptools-1.1-1 Tools for Handling Spatial Objectsmarkdown-1.1 Render Markdown with the C Library ‘Sundown’marray-1.70.0 Exploratory analysis for two-color spotted microarray datamatrixStats-0.58.0 Functions that Apply to Rows and Columns of Matrices (and to
Vectors)matrixcalc-1.0-3 Collection of Functions for Matrix CalculationsmaxLik-1.4-8 Maximum Likelihood Estimation and Related Toolsmaxlike-0.1-8 Model Species Distributions by Estimating the Probability of
Occurrence Using Presence-Only Datamaxnet-0.1.2 Fitting ‘Maxent’ Species Distribution Models with ‘glmnet’mboost-2.9-5 Model-Based Boostingmclust-5.4.7 Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimationmcmc-0.9-7 Markov Chain Monte Carlomcmcse-1.4-1 Monte Carlo Standard Errors for MCMCmda-0.5-2 Mixture and Flexible Discriminant Analysismedflex-0.6-7 Flexible Mediation Analysis Using Natural Effect Modelsmediation-4.5.0 Causal Mediation Analysismemoise-2.0.0 Memoisation of Functionsmemuse-4.1-0 Memory Estimation Utilitiesmetafor-2.4-0 Meta-Analysis Package for RmetagenomeSeq-1.34.0 Statistical analysis for sparse high-throughput sequencingmethods built in
methylKit-1.18.0 DNA methylation analysis from high-throughput bisulfite sequencing resultsmethylumi-2.38.0 Handle Illumina methylation datamets-1.2.8.1 Analysis of Multivariate Event Timesmgcv-1.8-35 Mixed GAM Computation Vehicle with Automatic Smoothness
Estimationmgsub-1.7.2 Safe, Multiple, Simultaneous String Substitutionmhsmm-0.4.16 Inference for Hidden Markov and Semi-Markov Modelsmi-1.0 Missing Data Imputation and Model Checkingmice-3.13.0 Multivariate Imputation by Chained Equationsmicrobenchmark-1.4-7 Accurate Timing Functionsmime-0.10 Map Filenames to MIME Typesminfi-1.38.0 Analyze Illumina Infinium DNA methylation arraysminiUI-0.1.1.1 Shiny UI Widgets for Small Screensminpack.lm-1.2-1 R Interface to the Levenberg-Marquardt Nonlinear Least-Squares
Algorithm Found in MINPACK, Plus Support for Boundsminqa-1.2.4 Derivative-free optimization algorithms by quadratic<U+000a>approximationmisc3d-0.9-0 Miscellaneous 3D PlotsmiscTools-0.6-26 Miscellaneous Tools and UtilitiesmissForest-1.4 Nonparametric Missing Value Imputation using Random Forestmitml-0.4-1 Tools for Multiple Imputation in Multilevel Modelingmitools-2.4 Tools for Multiple Imputation of Missing DatamixOmics-6.16.0 Omics Data Integration Projectmixsqp-0.3-43 Sequential Quadratic Programming for Fast Maximum-Likelihood
Estimation of Mixture Proportionsmixtools-1.2.0 Tools for Analyzing Finite Mixture Modelsmlbench-2.1-3 Machine Learning Benchmark Problemsmlegp-3.1.8 Maximum Likelihood Estimates of Gaussian Processesmlogit-1.1-1 Multinomial Logit Modelsmlr-2.19.0 Machine Learning in Rmltools-0.3.5 Machine Learning Toolsmnormt-2.0.2 The Multivariate Normal and t Distributions, and Their Truncated
Versionsmodeldata-0.1.0 Data Sets Used Useful for Modeling Packagesmodelr-0.1.8 Modelling Functions that Work with the Pipemodeltools-0.2-23 Tools and Classes for Statistical Modelsmoments-0.14 Moments, cumulants, skewness, kurtosis and related testsmondate-0.10.02 Keep Track of Dates in Terms of Monthsmotifmatchr-1.14.0 Fast Motif Matching in Rmpath-0.4-2.19 Regularized Linear Modelsmsa-1.24.0 Multiple Sequence Alignmentmsigdbr-7.4.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Formatmsm-1.6.8 Multi-State Markov and Hidden Markov Models in Continuous Timemultcomp-1.4-17 Simultaneous Inference in General Parametric Modelsmulticool-0.1-11 Permutations of Multisets in Cool-Lex Ordermulttest-2.48.0 Resampling-based multiple hypothesis testingmunsell-0.5.0 Utilities for Using Munsell Coloursmvabund-4.1.9 Statistical Methods for Analysing Multivariate Abundance Datamvnfast-0.2.5.1 Fast Multivariate Normal and Student’s t Methodsmvtnorm-1.1-1 Multivariate Normal and t Distributionsnabor-0.5.0 Wraps ‘libnabo’, a Fast K Nearest Neighbour Library for Low
Dimensionsnanotime-0.3.2 Nanosecond-Resolution Time Support for Rnatserv-1.0.0 ‘NatureServe’ Interfacencbit-2013.03.29 retrieve and build NBCI taxonomic datancdf4-1.17 Interface to Unidata netCDF (Version 4 or Earlier) Format Data
FilesncdfFlow-2.38.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.ndtv-0.13.0 Network Dynamic Temporal Visualizationsnetwork-1.16.1 Classes for Relational DatanetworkDynamic-0.10.1 Dynamic Extensions for Network Objectsnetworksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through
Sequential Importance SamplingneuRosim-0.2-12 Functions to Generate fMRI Data Including Activated Data, Noise
Data and Resting State Datangspatial-1.2-2 Fitting the Centered Autologistic and Sparse Spatial Generalized
Linear Mixed Models for Areal Datanleqslv-3.3.2 Solve Systems of Nonlinear Equationsnlme-3.1-152 Linear and Nonlinear Mixed Effects Modelsnloptr-1.2.2.2 R Interface to NLoptnlsem-0.8 Fitting Structural Equation Mixture Modelsnnet-7.3-16 Feed-Forward Neural Networks and Multinomial Log-Linear Modelsnnls-1.4 The Lawson-Hanson algorithm for non-negative least squares<U+000a>(NNLS)nonnest2-0.5-5 Tests of Non-Nested Modelsnor1mix-1.3-0 Normal aka Gaussian (1-d) Mixture Models (S3 Classes and
Methods)nortest-1.0-4 Tests for Normalitynp-0.60-10 Nonparametric Kernel Smoothing Methods for Mixed Data Typesnpsurv-0.5-0 Nonparametric Survival AnalysisnumDeriv-2016.8-1.1 Accurate Numerical Derivativesnumbers-0.8-2 Number-Theoretic Functionsnws-1.7.0.1 R functions for NetWorkSpaces and Sleighodbc-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)soligo-1.56.0 Preprocessing tools for oligonucleotide arraysoligoClasses-1.54.0 Classes for high-throughput arrays supported by oligo and crlmmopenCyto-2.4.0 Hierarchical Gating Pipeline for flow cytometry dataopenssl-1.4.4 Toolkit for Encryption, Signatures and Certificates Based on
OpenSSLopenxlsx-4.2.3 Read, Write and Edit xlsx Filesoperator.tools-1.6.3 Utilities for Working with R’s Operatorsoptimx-2020-4.2 Expanded Replacement and Extension of the ‘optim’ Functionoptmatch-0.9-13 Functions for Optimal Matchingoptparse-1.6.6 Command Line Option Parserordinal-2019.12-10 Regression Models for Ordinal Dataorg.Hs.eg.db-3.13.0 Genome wide annotation for Humanorg.Mm.eg.db-3.13.0 Genome wide annotation for Mouseoro.nifti-0.11.0 Rigorous - ‘NIfTI’ + ‘ANALYZE’ + ‘AFNI’ : Input / Outputorthopolynom-1.0-5 Collection of functions for orthogonal and orthonormal<U+000a>polynomialsoutliers-0.14 Tests for outlierspROC-1.17.0.1 Display and Analyze ROC Curvespack-0.1-1 Convert values to/from raw vectorspackrat-0.6.0 A Dependency Management System for Projects and their R Package
Dependenciespacman-0.5.1 Package Management Toolpamr-1.56.1 Pam: Prediction Analysis for Microarrayspan-1.6 Multiple Imputation for Multivariate Panel or Clustered DataparallelMap-1.5.0 Unified Interface to Parallelization Back-Endsparallelly-1.25.0 Enhancing the ‘parallel’ Packageparsedate-1.2.1 Recognize and Parse Dates in Various Formats, Including All ISO
8601 Formatsparsnip-0.1.6 A Common API to Modeling and Analysis Functionspartools-1.1.6 Tools for the ‘Parallel’ Packageparty-1.3-7 A Laboratory for Recursive Partytioningpartykit-1.2-13 A Toolkit for Recursive Partytioningpastecs-1.3.21 Package for Analysis of Space-Time Ecological Seriespatchwork-1.1.1 The Composer of Plotspathview-1.32.0 a tool set for pathway based data integration and visualizationpbapply-1.4-3 Adding Progress Bar to ‘*apply’ Functionspbivnorm-0.6.0 Vectorized Bivariate Normal CDFpbkrtest-0.5.1 Parametric Bootstrap, Kenward-Roger and Satterthwaite Based
Methods for Test in Mixed Modelspbs-1.1 Periodic B SplinespcaMethods-1.84.0 A collection of PCA methodspcaPP-1.9-74 Robust PCA by Projection Pursuitpdftools-3.0.1 Text Extraction, Rendering and Converting of PDF Documentspdist-1.2 Partitioned Distance Functionpedigree-1.4 Pedigree functionspedigreemm-0.3-3 Pedigree-based mixed-effects modelspenalized-0.9-51 L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
in GLMs and in the Cox Modelpeperr-1.3 Parallelised Estimation of Prediction Errorperm-1.0-0.0 Exact or Asymptotic permutation testspermute-0.9-5 Functions for Generating Restricted Permutations of Dataphangorn-2.7.0 Phylogenetic Reconstruction and Analysispheatmap-1.0.12 Pretty Heatmapsphylobase-0.8.10 Base Package for Phylogenetic Structures and Comparative Dataphyloseq-1.36.0 Handling and analysis of high-throughput microbiome census dataphytools-0.7-70 Phylogenetic Tools for Comparative Biology (and Other Things)pillar-1.6.1 Coloured Formatting for Columnspim-2.0.2 Fit Probabilistic Index Modelspinfsc50-1.2.0 Sequence (‘FASTA’), Annotation (‘GFF’) and Variants (‘VCF’) for
17 Samples of ‘P. Infestans” and 1 ‘P. Mirabilis’pixmap-0.4-12 Bitmap Images / Pixel Mapspkgbuild-1.2.0 Find Tools Needed to Build R Packagespkgconfig-2.0.3 Private Configuration for ‘R’ Packagespkgload-1.2.1 Simulate Package Installation and Attachpkgmaker-0.32.2 Development Utilities for R Packagesplogr-0.2.0 The ‘plog’ C++ Logging Libraryplot3D-1.3 Plotting Multi-Dimensional Dataplot3Drgl-1.0.1 Plotting Multi-Dimensional Data - Using ‘rgl’plotly-4.9.3 Create Interactive Web Graphics via ‘plotly.js’plotmo-3.6.0 Plot a Model’s Residuals, Response, and Partial Dependence Plotsplotrix-3.8-1 Various Plotting Functionspls-2.7-3 Partial Least Squares and Principal Component Regressionplyr-1.8.6 Tools for Splitting, Applying and Combining Datapng-0.1-7 Read and write PNG imagespoLCA-1.4.1 Polytomous variable Latent Class Analysispoisbinom-1.0.1 A Faster Implementation of the Poisson-Binomial Distributionpolspline-1.1.19 Polynomial Spline Routinespolyclip-1.10-0 Polygon Clippingpolyester-1.28.0 Simulate RNA-seq readspolynom-1.4-0 A Collection of Functions to Implement a Class for Univariate
Polynomial ManipulationspoweRlaw-0.70.6 Analysis of Heavy Tailed Distributionsprabclus-2.3-2 Functions for Clustering and Testing of Presence-Absence,
Abundance and Multilocus Genetic Datapracma-2.3.3 Practical Numerical Math Functionspraise-1.0.0 Praise UserspreprocessCore-1.54.0 A collection of pre-processing functionspreseqR-4.0.0 Predicting Species Accumulation Curvespresto 1.0.0
prettyunits-1.1.1 Pretty, Human Readable Formatting of Quantitiesprocessx-3.5.2 Execute and Control System Processesprodlim-2019.11.13 Product-Limit Estimation for Censored Event History AnalysisprofileModel-0.6.1 Profiling Inference Functions for Various Model Classesproftools-0.99-3 Profile Output Processing Tools for Rprogress-1.2.2 Terminal Progress Barsprojpred-2.0.2 Projection Predictive Feature Selectionpromises-1.2.0.1 Abstractions for Promise-Based Asynchronous Programmingproto-1.0.0 Prototype Object-Based Programmingproxy-0.4-25 Distance and Similarity Measurespryr-0.1.4 Tools for Computing on the Languageps-1.6.0 List, Query, Manipulate System Processespscl-1.5.5 Political Science Computational Laboratorypspline-1.0-18 Penalized Smoothing Splinespsych-2.1.3 Procedures for Psychological, Psychometric, and Personality
Researchpsychotools-0.6-1 Psychometric Modeling Infrastructurepulsar-0.3.7 Parallel Utilities for Lambda Selection along a Regularization
Pathpurrr-0.3.4 Functional Programming Toolspvclust-2.2-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap
ResamplingqdapRegex-0.7.2 Regular Expression Removal, Extraction, and Replacement Toolsqgam-1.3.3 Smooth Additive Quantile Regression Modelsqgraph-1.6.9 Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimationqpdf-1.1 Split, Combine and Compress PDF Filesqqman-0.1.8 Q-Q and Manhattan Plots for GWAS Dataqrnn-2.0.5 Quantile Regression Neural Networkqtl-1.48-1 Tools for Analyzing QTL Experimentsquadprog-1.5-8 Functions to Solve Quadratic Programming Problemsquantmod-0.4.18 Quantitative Financial Modelling Frameworkquantoptr-0.1.3 Algorithms for Quantile- And Mean-Optimal Treatment Regimesquantreg-5.85 Quantile Regressionquantsmooth-1.58.0 Quantile smoothing and genomic visualization of array dataquestionr-0.7.4 Functions to Make Surveys Processing Easierqvalue-2.24.0 Q-value estimation for false discovery rate controlqvcalc-1.0.2 Quasi Variances for Factor Effects in Statistical Modelsr2d3-0.2.5 Interface to ‘D3’ VisualizationsrARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD ProblemsrGADEM-2.40.0 de novo motif discoveryrJava-1.0-4 Low-Level R to Java Interfacerainbow-3.6 Bagplots, Boxplots and Rainbow Plots for Functional DatarandomForest-4.6-14 Breiman and Cutler’s Random Forests for Classification and
RegressionrandomForestSRC-2.11.0 Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)ranger-0.12.1 A Fast Implementation of Random Forestsrappdirs-0.3.3 Application Directories: Determine Where to Save Data, Caches,
and Logsraster-3.4-10 Geographic Data Analysis and Modelingrbenchmark-1.0.0 Benchmarking routine for Rrbibutils-2.1.1 Read ‘Bibtex’ Files and Convert Between Bibliography Formatsrcmdcheck-1.3.3 Run ‘R CMD check’ from ‘R’ and Capture Resultsrda-1.0.2-2.1 Shrunken Centroids Regularized Discriminant Analysisrdrop2-0.8.2.1 Programmatic Interface to the ‘Dropbox’ APIreadODS-1.7.0 Read and Write ODS Filesreadbitmap-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 Filesreadr-1.4.0 Read Rectangular Text Datareadxl-1.3.1 Read Excel Filesrecipes-0.1.16 Preprocessing Tools to Create Design MatricesrefGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from
‘Ensembl’ and ‘UCSC’ Genome Browsersrefund-0.1-23 Regression with Functional DataregioneR-1.24.0 Association analysis of genomic regions based on permutation testsregistry-0.5-1 Infrastructure for R Package Registriesregress-1.3-21 Gaussian Linear Models with Linear Covariance Structureregtools-1.1.0 Regression and Classification Toolsrelations-0.6-9 Data Structures and Algorithms for Relationsrelevent-1.0-4 Relational Event Modelsrematch-1.0.1 Match Regular Expressions with a Nicer ‘API’rematch2-2.1.2 Tidy Output from Regular Expression Matchingremotes-2.3.0 R Package Installation from Remote Repositories, Including
‘GitHub’rentrez-1.2.3 ‘Entrez’ in Rrepr-1.1.3 Serializable Representationsreprex-2.0.0 Prepare Reproducible Example Code via the Clipboardresample-0.4 Resampling Functionsreshape-0.8.8 Flexibly Reshape Datareshape2-1.4.4 Flexibly Reshape Data: A Reboot of the Reshape Packagerestfulr-0.0.13 R Interface to RESTful Web Servicesreticulate-1.20 Interface to ‘Python’rex-1.2.0 Friendly Regular Expressionsrgenoud-5.8-3.0 R Version of GENetic Optimization Using Derivativesrgexf-0.16.0 Build, Import and Export GEXF Graph Filesrgl-0.106.8 3D Visualization Using OpenGLrhdf5-2.36.0 R Interface to HDF5rhdf5filters-1.4.0 HDF5 Compression Filtersrio-0.5.26 A Swiss-Army Knife for Data I/Oritis-1.0.0 Integrated Taxonomic Information System Clientrjags-4-10 Bayesian Graphical Models using MCMCrjson-0.2.20 JSON for Rrlang-0.4.11 Functions for Base Types and Core R and ‘Tidyverse’ Featuresrle-0.9.2 Common Functions for Run-Length Encoded Vectorsrlecuyer-0.3-5 R Interface to RNG with Multiple Streamsrlist-0.4.6.1 A Toolbox for Non-Tabular Data Manipulationrmarkdown-2.8 Dynamic Documents for Rrmeta-3.0 Meta-Analysisrms-6.2-0 Regression Modeling Strategiesrncl-0.8.4 An Interface to the Nexus Class Libraryrngtools-1.5 Utility Functions for Working with Random Number Generatorsrobustbase-0.93-7 Basic Robust StatisticsrootSolve-1.8.2.1 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of
Ordinary Differential Equationsrotl-3.0.11 Interface to the ‘Open Tree of Life’ APIroxygen2-7.1.1 In-Line Documentation for Rrpart-4.1-15 Recursive Partitioning and Regression Treesrprojroot-2.0.2 Finding Files in Project Subdirectoriesrrcov-1.5-5 Scalable Robust Estimators with High Breakdown Pointrredlist-0.7.0 ‘IUCN’ Red List Clientrsample-0.1.0 General Resampling Infrastructurersconnect-0.8.17 Deployment Interface for R Markdown Documents and Shiny
Applicationsrslurm-0.6.0 Submit R Calculations to a ‘Slurm’ Clusterrstan-2.21.2 R Interface to Stanrstanarm-2.21.1 Bayesian Applied Regression Modeling via Stanrstantools-2.1.1 Tools for Developing R Packages Interfacing with ‘Stan’rstatix-0.7.0 Pipe-Friendly Framework for Basic Statistical Testsrstudioapi-0.13 Safely Access the RStudio APIrsvd-1.0.5 Randomized Singular Value Decompositionrsvg-2.1.2 Render SVG Images into PDF, PNG, PostScript, or Bitmap Arraysrtracklayer-1.52.0 R interface to genome annotation files and the UCSC genome browserruv-0.9.7.1 Detect and Remove Unwanted Variation using Negative Controlsrvcheck-0.1.8 R/Package Version Checkrversions-2.0.2 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’rvest-1.0.0 Easily Harvest (Scrape) Web Pagesrzmq-0.9.8 R Bindings for ‘ZeroMQ’sampling-2.9 Survey Samplingsamr-3.0 SAM: Significance Analysis of Microarrayssandwich-3.0-1 Robust Covariance Matrix Estimatorssass-0.4.0 Syntactically Awesome Style Sheets (‘Sass’)scales-1.1.1 Scale Functions for VisualizationscarHRD 1.0
scattermore-0.7 Scatterplots with More Pointsscatterpie-0.1.6 Scatter Pie Plotscatterplot3d-0.3-41 3D Scatter Plotschoolmath-0.4 Functions and datasets for math used in schoolscidb-3.0.0 An R Interface to SciDBscrime-1.3.5 Analysis of High-Dimensional Categorical Data Such as SNP Datasctransform-0.3.2 Variance Stabilizing Transformations for Single Cell UMI Dataseewave-2.1.6 Sound Analysis and Synthesissegmented-1.3-4 Regression Models with Break-Points / Change-Points Estimationselectr-0.4-2 Translate CSS Selectors to XPath Expressionssem-3.1-11 Structural Equation ModelssendmailR-1.2-1 send email using Rsensemakr-0.1.3 Sensitivity Analysis Tools for Regression ModelsseqLogo-1.58.0 Sequence logos for DNA sequence alignmentsseqinr-4.2-5 Biological Sequences Retrieval and Analysisseqminer-8.0 Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into Rsequenza-3.0.0 Copy Number Estimation from Tumor Genome Sequencing Dataservr-0.22 A Simple HTTP Server to Serve Static Files or Dynamic Documentssessioninfo-1.1.1 R Session Informationsets-1.0-18 Sets, Generalized Sets, Customizable Sets and Intervalssfsmisc-1.1-11 Utilities from ‘Seminar fuer Statistik’ ETH Zurichshadowtext-0.0.8 Shadow Text Grob and Layershape-1.4.6 Functions for Plotting Graphical Shapes, Colorsshapefiles-0.7 Read and Write ESRI Shapefilesshiny-1.6.0 Web Application Framework for RshinyBS-0.61 Twitter Bootstrap Components for ShinyshinyFiles-0.9.0 A Server-Side File System Viewer for Shinyshinycssloaders-1.0.0 Add Loading Animations to a ‘shiny’ Output While It’s
Recalculatingshinydashboard-0.7.1 Create Dashboards with ‘Shiny’shinyjs-2.0.0 Easily Improve the User Experience of Your Shiny Apps in Secondsshinystan-2.5.0 Interactive Visual and Numerical Diagnostics and Posterior
Analysis for Bayesian Modelsshinythemes-1.2.0 Themes for Shinysiggenes-1.66.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approachessignal-0.7-6 Signal Processingsitmo-2.0.1 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header
Filesslam-0.1-48 Sparse Lightweight Arrays and Matricesslider-0.2.1 Sliding Window Functionssm-2.2-5.6 Smoothing Methods for Nonparametric Regression and Density
EstimationsmfishHmrf-0.1 Hidden Markov Random Field for Spatial Transcriptomic Datasmoother-1.1 Functions Relating to the Smoothing of Numerical Datasn-2.0.0 The Skew-Normal and Related Distributions Such as the Skew-t and
the SUNsna-2.6 Tools for Social Network Analysissnow-0.4-3 Simple Network of Workstationssnowfall-1.84-6.1 Easier cluster computing (based on snow).snpStats-1.42.0 SnpMatrix and XSnpMatrix classes and methodssolrium-1.2.0 General Purpose R Interface to ‘Solr’som-0.3-5.1 Self-Organizing Mapsourcetools-0.1.7 Tools for Reading, Tokenizing and Parsing R Codesp-1.4-5 Classes and Methods for Spatial DataspData-0.3.8 Datasets for Spatial AnalysisspaMM-3.7.34 Mixed-Effect Models, Particularly Spatial Modelsspaa-0.2.2 SPecies Association Analysisspam-2.6-0 SPArse Matrixsparklyr-1.7.0 R Interface to Apache SparksparseMatrixStats-1.4.0 Summary Statistics for Rows and Columns of Sparse Matricesspatial-7.3-14 Functions for Kriging and Point Pattern Analysisspatstat-2.1-0 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Testsspatstat.core-2.1-2 Core Functionality of the ‘spatstat’ Familyspatstat.data-2.1-0 Datasets for ‘spatstat’ Familyspatstat.geom-2.1-0 Geometrical Functionality of the ‘spatstat’ Familyspatstat.linnet-2.1-1 Linear Networks Functionality of the ‘spatstat’ Familyspatstat.sparse-2.0-0 Sparse Three-Dimensional Arrays and Linear Algebra Utilitiesspatstat.utils-2.1-0 Utility Functions for ‘spatstat’splines built in
splitstackshape-1.4.8 Stack and Reshape Datasets After Splitting Concatenated Valuesspls-2.2-3 Sparse Partial Least Squares (SPLS) Regression and
Classificationsqldf-0.4-11 Manipulate R Data Frames Using SQLsquash-1.0.9 Color-Based Plots for Multivariate Visualizationssgraph-1.12 Bayesian Graphical Estimation using Spike-and-Slab Priorsstabledist-0.7-1 Stable Distribution Functionsstabs-0.6-4 Stability Selection with Error Controlstargazer-5.2.2 Well-Formatted Regression and Summary Statistics Tablesstartupmsg-0.9.6 Utilities for Start-Up Messagesstatmod-1.4.36 Statistical Modelingstatnet-2019.6 Software Tools for the Statistical Analysis of Network Datastatnet.common-4.4.1 Common R Scripts and Utilities Used by the Statnet Project
Softwarestats built in
stats4 built in
stdReg-3.4.1 Regression Standardizationstopwords-2.2 Multilingual Stopword Listsstringdist-0.9.6.3 Approximate String Matching, Fuzzy Text Search, and String
Distance Functionsstringi-1.6.2 Character String Processing Facilitiesstringr-1.4.0 Simple, Consistent Wrappers for Common String Operationsstrucchange-1.5-2 Testing, Monitoring, and Dating Structural Changesstyler-1.4.1 Non-Invasive Pretty Printing of R Codesubplex-1.6 Unconstrained Optimization using the Subplex Algorithmsurvey-4.0 Analysis of Complex Survey Samplessurvival-3.2-11 Survival AnalysissurvivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival datasva-3.40.0 Surrogate Variable Analysissvd-0.5 Interfaces to Various State-of-Art SVD and Eigensolverssys-3.4 Powerful and Reliable Tools for Running System Commands in RsystemPipeR-1.26.2 systemPipeR: NGS workflow and report generation environmentsystemfonts-1.0.2 System Native Font Findingtableone-0.12.0 Create ‘Table 1’ to Describe Baseline Characteristics with or
without Propensity Score Weightstables-0.9.6 Formula-Driven Table Generationtaxize-0.9.99 Taxonomic Information from Around the Webtcltk2-1.2-11 Tcl/Tk Additionstclust-1.4-2 Robust Trimmed Clusteringtensor-1.5 Tensor product of arraystensorA-0.36.2 Advanced Tensor Arithmetic with Named Indicestergm-3.7.0 Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph ModelstergmLite-2.2.1 Fast Simulation of Simple Temporal Exponential Random Graph
Modelstestit-0.13 A Simple Package for Testing R Packagestestthat-3.0.2 Unit Testing for Rthreejs-0.3.3 Interactive 3D Scatter Plots, Networks and Globestibble-3.1.2 Simple Data Framestictoc-1.0.1 Functions for Timing R Scripts, as Well as Implementations of
Stack and List Structurestidygraph-1.2.0 A Tidy API for Graph Manipulationtidymodels-0.1.3 Easily Install and Load the ‘Tidymodels’ Packagestidyposterior-0.1.0 Bayesian Analysis to Compare Models using Resampling Statisticstidypredict-0.4.8 Run Predictions Inside the Databasetidyr-1.1.3 Tidy Messy Datatidyselect-1.1.1 Select from a Set of Stringstidytext-0.3.1 Text Mining using ‘dplyr’, ‘ggplot2’, and Other Tidy Toolstidytree-0.3.4 A Tidy Tool for Phylogenetic Tree Data Manipulationtidyverse-1.3.1 Easily Install and Load the ‘Tidyverse’tiff-0.1-8 Read and Write TIFF ImagestilingArray-1.70.0 Transcript mapping with high-density oligonucleotide tiling arraystimeDate-3043.102 Rmetrics - Chronological and Calendar ObjectstimeSeries-3062.100 Financial Time Series Objects (Rmetrics)timereg-1.9.9 Flexible Regression Models for Survival Datatinytex-0.31 Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX DocumentstkWidgets-1.70.0 R based tk widgetstkrplot-0.0-25 TK Rplottm-0.7-8 Text Mining Packagetmle-1.5.0-1 Targeted Maximum Likelihood Estimationtmvnsim-1.0-2 Truncated Multivariate Normal Simulationtmvtnorm-1.4-10 Truncated Multivariate Normal and Student t Distributiontokenizers-0.2.1 Fast, Consistent Tokenization of Natural Language Texttools built in
topicmodels-0.2-12 Topic Modelstree-1.0-40 Classification and Regression Treestreeio-1.16.1 Base Classes and Functions for Phylogenetic Tree Input and Outputtriebeard-0.3.0 ‘Radix’ Trees in ‘Rcpp’trimcluster-0.1-5 Cluster Analysis with Trimmingtripack-1.3-9.1 Triangulation of Irregularly Spaced Datatruncnorm-1.0-8 Truncated Normal Distributiontrust-0.1-8 Trust Region Optimizationtseries-0.10-48 Time Series Analysis and Computational FinancetseriesChaos-0.1-13.1 Analysis of Nonlinear Time Seriestsna-0.3.3 Tools for Temporal Social Network Analysistsne-0.1-3 T-Distributed Stochastic Neighbor Embedding for R (t-SNE)tune-0.1.5 Tidy Tuning ToolstuneR-1.3.3 Analysis of Music and Speechtweedie-2.3.3 Evaluation of Tweedie Exponential Family Modelstweenr-1.0.2 Interpolate Data for Smooth Animationsucminf-1.1-4 General-Purpose Unconstrained Non-Linear Optimizationudunits2-0.13 Udunits-2 Bindings for Runbalanced-2.0 Racing for Unbalanced Methods SelectionuniqueAtomMat-0.1-3-2 Finding Unique or Duplicated Rows or Columns for Atomic Matricesunits-0.7-1 Measurement Units for R Vectorsunmarked-1.1.0 Models for Data from Unmarked Animalsurca-1.3-0 Unit Root and Cointegration Tests for Time Series Dataurltools-1.7.3 Vectorised Tools for URL Handling and Parsinguroot-2.1-2 Unit Root Tests for Seasonal Time Seriesusethis-2.0.1 Automate Package and Project Setuputf8-1.2.1 Unicode Text Processingutils built in
uuid-0.1-4 Tools for Generating and Handling of UUIDsuwot-0.1.10 The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reductionvcd-1.4-8 Visualizing Categorical DatavcfR-1.12.0 Manipulate and Visualize VCF Datavctrs-0.3.8 Vector Helpersvegan-2.5-7 Community Ecology Packagevenn-1.10 Draw Venn Diagramsvimp-2.2.1 Perform Inference on Algorithm-Agnostic Variable Importancevioplot-0.3.6 Violin Plotvipor-0.4.5 Plot Categorical Data Using Quasirandom Noise and Density
Estimatesviridis-0.6.1 Colorblind-Friendly Color Maps for RviridisLite-0.4.0 Colorblind-Friendly Color Maps (Lite Version)visNetwork-2.0.9 Network Visualization using ‘vis.js’ Libraryvsn-3.60.0 Variance stabilization and calibration for microarray datawaldo-0.2.5 Find Differences Between R Objectswarp-0.2.0 Group Dateswaveslim-1.8.2 Basic Wavelet Routines for One-, Two-, and Three-Dimensional
Signal Processingwavethresh-4.6.8 Wavelets Statistics and Transformswebp-1.0 A New Format for Lossless and Lossy Image Compressionwebshot-0.5.2 Take Screenshots of Web Pageswhisker-0.4 for R, Logicless TemplatingwidgetTools-1.70.0 Creates an interactive tcltk widgetwikitaxa-0.4.0 Taxonomic Information from ‘Wikipedia’withr-2.4.2 Run Code ‘With’ Temporarily Modified Global Statewordcloud-2.6 Word Cloudsworkflows-0.2.2 Modeling Workflowsworkflowsets-0.0.2 Create a Collection of ‘tidymodels’ Workflowsworrms-0.4.2 World Register of Marine Species (WoRMS) ClientxCell 1.1.0
xfun-0.23 Supporting Functions for Packages Maintained by ‘Yihui Xie’xgboost-1.4.1.1 Extreme Gradient Boostingxlsx-0.6.5 Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Filesxlsxjars-0.6.1 Package required POI jars for the xlsx packagexml2-1.3.2 Parse XMLxmlparsedata-1.0.5 Parse Data of ‘R’ Code as an ‘XML’ Treexopen-1.0.0 Open System Files, ‘URLs’, Anythingxtable-1.8-4 Export Tables to LaTeX or HTMLxts-0.12.1 eXtensible Time SeriesyaImpute-1.0-32 Nearest Neighbor Observation Imputation and Evaluation Toolsyaml-2.2.1 Methods to Convert R Data to YAML and Backyardstick-0.0.8 Tidy Characterizations of Model PerformancezCompositions-1.3.4 Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Setszeallot-0.1.0 Multiple, Unpacking, and Destructuring Assignmentzip-2.1.1 Cross-Platform ‘zip’ Compressionzlibbioc-1.38.0 An R packaged zlib-1.2.5zoo-1.8-9 S3 Infrastructure for Regular and Irregular Time Series (Z’s
Ordered Observations)