Known Issues
None
Package List
ADGofTest-0.3 Anderson-Darling GoF testALDEx2-1.14.1 Analysis Of Differential Abundance Taking Sample Variation Into AccountASCAT 2.5.2
AUC-0.3.0 Threshold independent performance measures for probabilistic<U+000a>classifiers.AgiMicroRna-2.32.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAlgDesign-1.1-7.3 Algorithmic Experimental DesignAnnotationDbi-1.44.0 Annotation Database InterfaceAnnotationFilter-1.6.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.24.0 Code for Building Annotation Database PackagesAnnotationHub-2.14.4 Client to access AnnotationHub resourcesBB-2014.10-1 Solving and Optimizing Large-Scale Nonlinear SystemsBBmisc-1.11 Miscellaneous Helper Functions for B. BischlBDgraph-2.53 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMCBH-1.66.0-1 Boost C++ Header FilesBSgenome-1.50.0 Software infrastructure for efficient representation of full genomes and their SNPsBSgenome.Hsapiens.UCSC.hg19-1.4.0 Full genome sequences for Homo sapiens (UCSC version hg19)BatchJobs-1.7 Batch Computing with RBayesianTools-0.1.5 General-Purpose MCMC and SMC Samplers and Tools for Bayesian
StatisticsBhat-0.9-10 General likelihood explorationBiasedUrn-1.07 Biased Urn Model DistributionsBiobase-2.42.0 Biobase: Base functions for BioconductorBiocGenerics-0.28.0 S4 generic functions for BioconductorBiocInstaller-1.32.1 Install/Update Bioconductor, CRAN, and github PackagesBiocManager-1.30.4 Access the Bioconductor Project Package RepositoryBiocParallel-1.16.6 Bioconductor facilities for parallel evaluationBiostrings-2.50.2 Efficient manipulation of biological stringsBivarP-1.0 Estimating the Parameters of Some Bivariate DistributionsBolstad-0.2-40 Functions for Elementary Bayesian InferenceBolstad2-1.0-28 Bolstad functionsBradleyTerry2-1.0-9 Bradley-Terry ModelsBrobdingnag-1.2-6 Very Large Numbers in RCGEN-3.18.0 An R package for analysis of case-control studies in genetic epidemiologyCGHbase-1.42.0 CGHbase: Base functions and classes for arrayCGH data analysis.CVST-0.2-2 Fast Cross-Validation via Sequential TestingCairo-1.5-9 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-2.48.1 Category AnalysisComICS-1.0.4 Computational Methods for Immune Cell-Type SubsetsCompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal VariablesDAAG-1.22.1 Data Analysis and Graphics Data and FunctionsDBI-1.0.0 R Database InterfaceDEGseq-1.36.1 Identify Differentially Expressed Genes from RNA-seq dataDESeq-1.34.1 Differential gene expression analysis based on the negative binomial distributionDESeq2-1.22.2 Differential gene expression analysis based on the negative binomial distributionDEoptimR-1.0-8 Differential Evolution Optimization in Pure RDHARMa-0.2.0 Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression ModelsDNAcopy-1.56.0 DNA copy number data analysisDRR-0.0.3 Dimensionality Reduction via RegressionDT-0.5 A Wrapper of the JavaScript Library ‘DataTables’DTRreg-1.3 DTR Estimation and Inference via G-Estimation, Dynamic WOLS, and
Q-LearningDelayedArray-0.8.0 Delayed operations on array-like objectsDelayedMatrixStats-1.4.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ ObjectsDeriv-3.8.5 Symbolic DifferentiationDiagrammeR-1.0.0 Graph/Network VisualizationDiffBind-2.10.0 Differential Binding Analysis of ChIP-Seq Peak DataDiscriMiner-0.1-29 Tools of the Trade for Discriminant AnalysisDistributionUtils-0.6-0 Distribution UtilitiesDynDoc-1.60.0 Dynamic document toolsEBImage-4.24.0 Image processing and analysis toolbox for REasyABC-1.5 Efficient Approximate Bayesian Computation Sampling SchemesEpiModel-1.7.2 Mathematical Modeling of Infectious Disease DynamicsFDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probesFME-1.3.5 A Flexible Modelling Environment for Inverse Modelling,
Sensitivity, Identifiability and Monte Carlo AnalysisFNN-1.1.2.2 Fast Nearest Neighbor Search Algorithms and ApplicationsFactoMineR-1.41 Multivariate Exploratory Data Analysis and Data MiningFormula-1.2-3 Extended Model FormulasGENESIS-2.12.4 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessGEOquery-2.50.5 Get data from NCBI Gene Expression Omnibus (GEO)GGally-1.4.0 Extension to ‘ggplot2’GO.db-3.7.0 A set of annotation maps describing the entire Gene OntologyGOstats-2.48.0 Tools for manipulating GO and microarraysGSA-1.03 Gene Set AnalysisGSEABase-1.44.0 Gene set enrichment data structures and methodsGUTS-1.1.0 Fast Calculation of the Likelihood of a Stochastic Survival
ModelGWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association StudiesGenSA-1.1.7 Generalized Simulated AnnealingGeneNet-1.2.13 Modeling and Inferring Gene NetworksGenomeGraphs-1.42.0 Plotting genomic information from EnsemblGenomeInfoDb-1.18.2 Utilities for manipulating chromosome and other ‘seqname’ identifiersGenomeInfoDbData-1.2.0 Species and taxonomy ID look up tables used by GenomeInfoDbGenomicAlignments-1.18.1 Representation and manipulation of short genomic alignmentsGenomicFeatures-1.34.4 Tools for making and manipulating transcript centric annotationsGenomicFiles-1.18.0 Distributed computing by file or by rangeGenomicRanges-1.34.0 Representation and manipulation of genomic intervals and variables defined along a genomeGetoptLong-0.1.7 Parsing Command-Line Arguments and Variable InterpolationGillespieSSA-0.5-4 Gillespie’s Stochastic Simulation Algorithm (SSA)GlobalOptions-0.1.0 Generate Functions to Get or Set Global OptionsGviz-1.26.5 Plotting data and annotation information along genomic coordinatesHCsnip 1.16.0
HDF5Array-1.10.1 HDF5 backend for DelayedArray objectsHMMcopy-1.24.0 Copy number prediction with correction for GC and mappability bias for HTS dataHWxtest-1.1.7 Exact Tests for Hardy-Weinberg ProportionsHaploSim-1.8.4 Functions to simulate haplotypesHmisc-4.1-1 Harrell MiscellaneousHomo.sapiens-1.3.1 Annotation package for the Homo.sapiens objectIDPmisc-1.1.18 ‘Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)’IRanges-2.16.0 Infrastructure for manipulating intervals on sequencesIRdisplay-0.7.0 ‘Jupyter’ Display MachineryIlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arraysIso-0.0-17 Functions to Perform Isotonic RegressionJBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J.
ButtlarKEGG.db-3.2.3 A set of annotation maps for KEGGKEGGREST-1.22.0 Client-side REST access to KEGGKEGGgraph-1.42.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorKEGGprofile-1.24.0 An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathwayKODAMA-1.5 Knowledge Discovery by Accuracy MaximizationKernSmooth-2.23-15 Functions for Kernel Smoothing Supporting Wand & Jones (1995)LearnBayes-2.15.1 Functions for Learning Bayesian InferenceLmoments-1.2-3 L-Moments and Quantile MixturesLogicReg-1.5.10 Logic RegressionLymphoSeq-1.10.0 Analyze high-throughput sequencing of T and B cell receptorsLymphoSeqDB-0.99.2 LymphoSeq annotation databasesMASS-7.3-51.1 Support Functions and Datasets for Venables and Ripley’s MASSMCMCglmm-2.28 MCMC Generalised Linear Mixed ModelsMCMCpack-1.4-4 Markov Chain Monte Carlo (MCMC) PackageMPV-1.53 Data Sets from Montgomery, Peck and ViningMatchIt-3.0.2 Nonparametric Preprocessing for Parametric Causal InferenceMatching-4.9-3 Multivariate and Propensity Score Matching with Balance
OptimizationMatrix-1.2-15 Sparse and Dense Matrix Classes and MethodsMatrixModels-0.4-1 Modelling with Sparse And Dense MatricesMfuzz-2.42.0 Soft clustering of time series gene expression dataModelMetrics-1.2.2 Rapid Calculation of Model MetricsMotIV-1.38.0 Motif Identification and ValidationNLP-0.2-0 Natural Language Processing InfrastructureNMF-0.21.0 Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)NOISeq-2.26.1 Exploratory analysis and differential expression for RNA-seq dataOceanView-1.0.4 Visualisation of Oceanographic Data and Model OutputOrganismDbi-1.24.0 Software to enable the smooth interfacing of different database packagesPBSddesolve-1.12.4 Solver for Delay Differential EquationsPFAM.db-3.7.0 A set of protein ID mappings for PFAMPICS-2.26.0 Probabilistic inference of ChIP-seqParamHelpers-1.11 Helpers for Parameters in Black-Box Optimization, Tuning and
Machine LearningPoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log
linear modelPolynomF-1.0-2 Polynomials in RPresenceAbsence-1.1.9 Presence-Absence Model Evaluation.ProtGenerics-1.14.0 S4 generic functions for Bioconductor proteomics infrastructureR.cache-0.13.0 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.methodsS3-1.7.1 S3 Methods SimplifiedR.oo-1.22.0 R Object-Oriented Programming with or without ReferencesR.rsp-0.43.0 Dynamic Generation of Scientific ReportsR.utils-2.7.0 Various Programming UtilitiesR2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’R2jags-0.5-7 Using R to Run ‘JAGS’R6-2.3.0 Encapsulated Classes with Reference SemanticsRANN-2.6 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
MetricRBGL-1.58.1 An interface to the BOOST graph libraryRCircos-1.2.0 Circos 2D Track PlotRColorBrewer-1.1-2 ColorBrewer PalettesRCurl-1.95-4.11 General Network (HTTP/FTP/…) Client Interface for RREDCapR-0.9.8 Interaction Between R and REDCapRGCCA-2.1.2 Regularized and Sparse Generalized Canonical Correlation
Analysis for Multiblock DataRInside-0.2.14 C++ Classes to Embed R in C++ ApplicationsRItools-0.1-16 Randomization Inference ToolsRJSONIO-1.3-1.1 Serialize R Objects to JSON, JavaScript Object NotationRLRsim-3.1-3 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
ModelsRMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix<U+000a>TheoryRMySQL-0.10.17 Database Interface and ‘MySQL’ Driver for RRNASeqPower-1.22.1 Sample size for RNAseq studiesRNeXML-2.2.0 Semantically Rich I/O for the ‘NeXML’ FormatROCR-1.0-7 Visualizing the Performance of Scoring ClassifiersRPostgreSQL-0.6-2 R Interface to the ‘PostgreSQL’ Database SystemRProtoBufLib-1.4.0 C++ headers and static libraries of Protocol buffersRSNNS-0.4-11 Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)RSQLite-2.1.1 ‘SQLite’ Interface for RRSpectra-0.13-1 Solvers for Large-Scale Eigenvalue and SVD ProblemsRUnit-0.4.32 R Unit Test FrameworkRWeka-0.4-39 R/Weka InterfaceRWekajars-3.9.3-1 R/Weka Interface JarsRcpp-1.0.0 Seamless R and C++ IntegrationRcppArmadillo-0.9.200.5.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra
LibraryRcppEigen-0.3.3.5.0 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra
LibraryRcppGSL-0.3.6 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and MatricesRcppParallel-4.4.2 Parallel Programming Tools for ‘Rcpp’RcppProgress-0.4.1 An Interruptible Progress Bar with OpenMP Support for C++ in R
PackagesRcppRoll-0.3.0 Efficient Rolling / Windowed OperationsRdpack-0.10-1 Update and Manipulate Rd Documentation ObjectsReportingTools-2.22.1 Tools for making reports in various formatsRglpk-0.6-4 R/GNU Linear Programming Kit InterfaceRgraphviz-2.26.0 Provides plotting capabilities for R graph objectsRhdf5lib-1.4.2 hdf5 library as an R packageRhpc-0.18-204 Permits *apply() Style Dispatch for ‘HPC’Ringo-1.46.0 R Investigation of ChIP-chip OligoarraysRlabkey-2.2.4 Data Exchange Between R and ‘LabKey’ ServerRmpi-0.6-9 Interface (Wrapper) to MPI (Message-Passing Interface)Rook-1.1-1 Rook - a web server interface for RRsamtools-1.34.1 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importRssa-1.0 A Collection of Methods for Singular Spectrum AnalysisRsubread-1.32.4 Subread sequence alignment and counting for RRtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
ImplementationRttf2pt1-1.3.7 ‘ttf2pt1’ ProgramS4Vectors-0.20.1 S4 implementation of vector-like and list-like objectsSDMTools-1.1-221 Species Distribution Modelling Tools: Tools for processing data
associated with species distribution modelling exercisesSKAT-1.3.2.1 SNP-Set (Sequence) Kernel Association TestSNPRelate-1.16.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)SPIA-2.34.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsSQUAREM-2017.10-1 Squared Extrapolation Methods for Accelerating EM-Like Monotone
AlgorithmsSeqArray-1.22.6 Data Management of Large-scale Whole-genome Sequence Variant CallsSeqVarTools-1.20.2 Tools for variant dataShortRead-1.40.0 FASTQ input and manipulationSimSeq-1.4.0 Nonparametric Simulation of RNA-Seq DataSparseM-1.77 Sparse Linear AlgebraStanHeaders-2.18.1 C++ Header Files for StanSummarizedExperiment-1.12.0 SummarizedExperiment containerSuperLearner-2.0-24 Super Learner PredictionSuppDists-1.1-9.4 Supplementary DistributionsTH.data-1.0-9 TH’s Data ArchiveTMB-1.7.15 Template Model Builder: A General Random Effect Tool Inspired by
‘ADMB’TTR-0.23-4 Technical Trading RulesTeachingDemos-2.10 Demonstrations for Teaching and LearningTitanCNA-1.20.1 Subclonal copy number and LOH prediction from whole genome sequencing of tumoursTraMineR-2.0-10 Trajectory Miner: a Toolbox for Exploring and Rendering
SequencesTxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)UpSetR-1.3.3 A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting SetsVGAM-1.0-6 Vector Generalized Linear and Additive ModelsVIM-4.7.0 Visualization and Imputation of Missing ValuesVariantAnnotation-1.28.13 Annotation of Genetic VariantsVennDiagram-1.6.20 Generate High-Resolution Venn and Euler PlotsWikidataR-1.4.0 API Client Library for ‘Wikidata’WikipediR-1.5.0 A MediaWiki API WrapperWriteXLS-4.0.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) FilesXML-3.98-1.16 Tools for Parsing and Generating XML Within R and S-PlusXVector-0.22.0 Representation and manipulation of external sequencesabc-2.1 Tools for Approximate Bayesian Computation (ABC)abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)abind-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 Baggingade4-1.7-13 Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciencesadegenet-2.1.1 Exploratory Analysis of Genetic and Genomic Dataadephylo-1.1-11 Exploratory Analyses for the Phylogenetic Comparative Methodaffy-1.60.0 Methods for Affymetrix Oligonucleotide Arraysaffycoretools-1.54.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChipsaffyio-1.52.0 Tools for parsing Affymetrix data filesaggregation-1.0.1 p-Value Aggregation Methodsakima-0.6-2 Interpolation of Irregularly and Regularly Spaced Dataalr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Editionamap-0.8-16 Another Multidimensional Analysis Packageanimation : 2.6 built in
annaffy-1.54.0 Annotation tools for Affymetrix biological metadataannotate-1.60.1 Annotation for microarraysaod-1.3 Analysis of Overdispersed Dataape-5.2 Analyses of Phylogenetics and Evolutionargparser-0.4 Command-Line Argument Parserarm-1.10-1 Data Analysis Using Regression and Multilevel/Hierarchical
Modelsaskpass-1.1 Safe Password Entry for R, Git, and SSHasnipe-1.1.11 Animal Social Network Inference and Permutations for Ecologistsassertthat-0.2.0 Easy Pre and Post Assertionsaudio-0.1-5.1 Audio Interface for Raws.ec2metadata-0.1.5 Get EC2 Instance Metadataaws.s3-0.3.12 ‘AWS S3’ Client Packageaws.signature-0.4.4 Amazon Web Services Request Signaturesbackports-1.1.3 Reimplementations of Functions Introduced Since R-3.0.0bartMachine-1.2.4.2 Bayesian Additive Regression TreesbartMachineJARs-1.1 bartMachine JARsbase built in
base64-2.0 Base64 Encoder and Decoderbase64enc-0.1-3 Tools for base64 encodingbaySeq-2.16.0 Empirical Bayesian analysis of patterns of differential expression in count databayesm-3.1-1 Bayesian Inference for Marketing/Micro-Econometricsbdsmatrix-1.3-3 Routines for Block Diagonal Symmetric Matricesbeanplot-1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin<U+000a>Plot)beeswarm-0.2.3 The Bee Swarm Plot, an Alternative to Stripchartbenchmark-0.3-6 Benchmark Experiments Toolboxbibtex-0.4.2 Bibtex Parserbiglm-0.9-1 bounded memory linear and generalized linear modelsbigmemory-4.5.33 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-2.3-4 Biological Structure Analysisbiom-0.3.12 An interface package (beta) for the BIOM file format.biomaRt-2.38.0 Interface to BioMart databases (i.e. Ensembl)biovizBase-1.30.1 Basic graphic utilities for visualization of genomic data.bit-1.1-14 A Class for Vectors of 1-Bit Booleansbit64-0.9-7 A S3 Class for Vectors of 64bit Integersbitops-1.0-6 Bitwise Operationsblob-1.1.1 A Simple S3 Class for Representing Vectors of Binary Data
(‘BLOBS’)bmp-0.3 Read Windows Bitmap (BMP) Imagesbnlearn-4.4 Bayesian Network Structure Learning, Parameter Learning and
Inferencebold-0.8.6 Interface to Bold Systems APIboot-1.3-20 Bootstrap Functions (Originally by Angelo Canty for S)bootstrap-2017.2 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-0.6.1 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-0.6-0 Bridge Sampling for Marginal Likelihoods and Bayes Factorsbroom-0.5.1 Convert Statistical Analysis Objects into Tidy Tibblesbst-0.3-15 Gradient Boostingbumphunter-1.24.5 Bump HuntercaTools-1.17.1.1 Tools: moving window statistics, GIF, Base64, ROC AUC, etc.calibrate-1.7.2 Calibration of Scatterplot and Biplot Axescallr-3.1.1 Call R from Rcar-3.0-2 Companion to Applied RegressioncarData-3.0-2 Companion to Applied Regression Data Setscaret-6.0-81 Classification and Regression Trainingcatdata-1.2.1 Categorical Datacellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columnscgdsr-1.2.10 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-1.8.5 Fast and Versatile Argument Checkschemometrics-1.4.2 Multivariate Statistical Analysis in Chemometricschipseq-1.32.0 chipseq: A package for analyzing chipseq datachron-2.3-53 Chronological Objects which can Handle Dates and Timescirclize-0.4.5 Circular VisualizationclValid-0.6-6 Validation of Clustering Resultsclass-7.3-14 Functions for ClassificationclassInt-0.3-1 Choose Univariate Class Intervalscli-1.0.1 Helpers for Developing Command Line Interfacesclipr-0.4.1 Read and Write from the System Clipboardclisymbols-1.2.0 Unicode Symbols at the R Promptclue-0.3-57 Cluster Ensemblescluster-2.0.7-1 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et
al.clusterGeneration-1.3.4 Random Cluster Generation (with Specified Degree of Separation)clusterRepro-0.9 Reproducibility of Gene Expression Clustersclustree-0.2.2 Visualise Clusterings at Different Resolutionscoda-0.19-2 Output Analysis and Diagnostics for MCMCcodetools-0.2-16 Code Analysis Tools for Rcoin-1.2-2 Conditional Inference Procedures in a Permutation Test Frameworkcolorspace-1.3-2 A Toolbox for Manipulating and Assessing Colors and Palettescolourpicker-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-1.40-2 Compositional Data Analysisconfig-0.3 Manage Environment Specific Configuration Valuescopula-0.999-19 Multivariate Dependence with Copulascorpcor-1.6.9 Efficient Estimation of Covariance and (Partial) Correlationcowplot-0.9.3 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’coxme-2.2-10 Mixed Effects Cox Modelscrayon-1.3.4 Colored Terminal Outputcrosstalk-1.0.0 Inter-Widget Interactivity for HTML Widgetscrul-0.6.0 HTTP ClientcsSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarrayscubature-2.0.3 Adaptive Multivariate Integration over HypercubescummeRbund-2.24.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.curl-3.2 A Modern and Flexible Web Client for RcvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervalscytolib-1.4.1 C++ infrastructure for representing and interacting with the gated cytometryd3Network-0.5.2.1 Tools for creating D3 JavaScript network, tree, dendrogram, and<U+000a>Sankey graphs from Rdata.table-1.11.8 Extension of data.framedatasets built in
dbplyr-1.2.2 A ‘dplyr’ Back End for Databasesddalpha-1.3.7 Depth-Based Classification and Calculation of Data DepthdeSolve-1.21 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-0.1-15 Delaunay Triangulation and Dirichlet (Voronoi) Tessellationdendextend-1.9.0 Extending ‘dendrogram’ Functionality in Rderfinder-1.16.1 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approachderfinderHelper-1.16.1 derfinder helper packagedesc-1.2.0 Manipulate DESCRIPTION Filesdescr-1.1.4 Descriptive Statisticsdevtools-2.0.1 Tools to Make Developing R Packages Easierdfoptim-2018.2-1 Derivative-Free Optimizationdiagram-1.6.4 Functions for Visualising Simple Graphs (Networks), Plotting
Flow Diagramsdiamonds-1.0-5 Analysis and sampling grids from diamond partitionsdichromat-2.0-0 Color Schemes for Dichromatsdigest-0.6.18 Create Compact Hash Digests of R ObjectsdimRed-0.2.2 A Framework for Dimensionality Reductiondiptest-0.75-7 Hartigan’s Dip Test Statistic for Unimodality - Correcteddismo-1.1-4 Species Distribution Modelingdistillery-1.0-4 Method Functions for Confidence Intervals and to Distill
Information from an Objectdistr-2.7.0 Object Oriented Implementation of DistributionsdistrEx-2.7.0 Extensions of Package ‘distr’diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis
PackagedoMC-1.3.5 Foreach Parallel Adaptor for ‘parallel’doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi PackagedoParallel-1.0.14 Foreach Parallel Adaptor for the ‘parallel’ PackagedoRNG-1.7.1 Generic Reproducible Parallel Backend for ‘foreach’ LoopsdoSNOW-1.0.16 Foreach Parallel Adaptor for the ‘snow’ PackagedotCall64-1.0-0 Enhanced Foreign Function Interface Supporting Long Vectorsdownloader-0.4 Download Files over HTTP and HTTPSdplyr-0.7.8 A Grammar of Data Manipulationdtangle-0.3.1 Cell Type Deconvolution from Gene Expressionsdtw-1.20-1 Dynamic Time Warping Algorithmsdummies-1.5.6 Create dummy/indicator variables flexibly and efficientlydynamicTreeCut-1.63-1 Methods for Detection of Clusters in Hierarchical Clustering
Dendrogramse1071-1.7-0 Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU WienedgeR-3.24.3 Empirical Analysis of Digital Gene Expression Data in Relasticnet-1.1.1 Elastic-Net for Sparse Estimation and Sparse PCAellipse-0.4.1 Functions for Drawing Ellipses and Ellipse-Like Confidence
Regionsellipsis-0.1.0 Tools for Working with …emulator-1.2-17 Bayesian Emulation of Computer Programsenergy-1.7-5 E-Statistics: Multivariate Inference via the Energy of Dataensembldb-2.6.7 Utilities to create and use Ensembl-based annotation databasesergm-3.9.4 Fit, Simulate and Diagnose Exponential-Family Models for
Networksergm.count-3.3.0 Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edgesevaluate-0.12 Parsing and Evaluation Tools that Provide More Details than the
Defaultexpm-0.999-3 Matrix Exponential, Log, ‘etc’expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”extRemes-2.0-9 Extreme Value Analysisextrafont-0.17 Tools for using fontsextrafontdb-1.0 Package for holding the database for the extrafont packagefail-1.3 File Abstraction Interface Layer (FAIL)fansi-0.4.0 ANSI Control Sequence Aware String Functionsfarver-1.1.0 Vectorised Colour Conversion and ComparisonfastICA-1.2-1 FastICA Algorithms to Perform ICA and Projection Pursuitfastcluster-1.1.25 Fast Hierarchical Clustering Routines for R and ‘Python’fastmatch-1.1-0 Fast match() functionfastseg-1.28.0 fastseg - a fast segmentation algorithmfasttime-1.0-2 Fast Utility Function for Time Parsing and Conversionfda-2.4.8 Functional Data Analysisfdrtool-1.2.15 Estimation of (Local) False Discovery Rates and Higher Criticismfeather-0.3.1 R Bindings to the Feather ‘API’ff-2.2-14 Memory-Efficient Storage of Large Data on Disk and Fast Access
Functionsffbase-0.12.7 Basic Statistical Functions for Package ‘ff’fftw-1.0-4 Fast FFT and DCT Based on the FFTW Libraryfftwtools-0.9-8 Wrapper for ‘FFTW3’ Includes: One-Dimensional Univariate,
One-Dimensional Multivariate, and Two-Dimensional Transformfields-9.6 Tools for Spatial Datafilehash-2.4-1 Simple Key-Value DatabasefishMod-0.29 Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta
Log-Normal Modelsfit.models-0.5-14 Compare Fitted Modelsfitdistrplus-1.0-11 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-2.3-14 Flexible Mixture ModelingflowClust-3.20.1 Clustering for Flow CytometryflowCore-1.48.1 flowCore: Basic structures for flow cytometry dataflowStats-3.40.1 Statistical methods for the analysis of flow cytometry dataflowViz-1.46.1 Visualization for flow cytometryflowWorkspace-3.30.2 Infrastructure for representing and interacting with gated and ungated cytometry data sets.fma-2.3 Data Sets from “Forecasting: Methods and Applications” by
Makridakis, Wheelwright & Hyndman (1998)forcats-0.3.0 Tools for Working with Categorical Variables (Factors)foreach-1.4.4 Provides Foreach Looping Construct for Rforecast-8.4 Forecasting Functions for Time Series and Linear Modelsforeign-0.8-71 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’,
‘Systat’, ‘Weka’, ‘dBase’, …forge-0.2.0 Casting Values into ShapeformatR-1.5 Format R Code Automaticallyfossil-0.3.7 Palaeoecological and Palaeogeographical Analysis Toolsfpc-2.1-11.1 Flexible Procedures for Clusteringfpp-0.5 Data for “Forecasting: principles and practice”fracdiff-1.4-2 Fractionally differenced ARIMA aka ARFIMA(p,d,q) modelsfs-1.2.6 Cross-Platform File System Operations Based on ‘libuv’fts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)futile.logger-1.4.3 A Logging Utility for Rfutile.options-1.0.1 Futile Options Managementfuture-1.10.0 Unified Parallel and Distributed Processing in R for Everyonegage-2.32.1 Generally Applicable Gene-set Enrichment for Pathway Analysisgam-1.16 Generalized Additive Modelsgamlss-5.1-2 Generalised Additive Models for Location Scale and Shapegamlss.data-5.1-0 GAMLSS Datagamlss.dist-5.1-1 Distributions for Generalized Additive Models for Location Scale
and Shapegamlss.tr-5.1-0 Generating and Fitting Truncated `gamlss.family’ Distributionsgamm4-0.2-5 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’gap-1.1-22 Genetic Analysis Packagegapfill-0.9.6 Fill Missing Values in Satellite DatagbRd-0.4-11 Utilities for processing Rd objects and filesgbm-2.1.4 Generalized Boosted Regression Modelsgclus-1.3.1 Clustering Graphicsgcrma-2.54.0 Background Adjustment Using Sequence InformationgdalUtils-2.0.1.14 Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilitiesgdata-2.18.0 Various R Programming Tools for Data Manipulationgdistance-1.2-2 Distances and Routes on Geographical Gridsgdsfmt-1.18.1 R Interface to CoreArray Genomic Data Structure (GDS) filesgee-4.13-19 Generalized Estimation Equation Solvergeepack-1.2-1 Generalized Estimating Equation Packagegeiger-2.0.6 Analysis of Evolutionary DiversificationgeneLenDataBase-1.18.0 Lengths of mRNA transcripts for a number of genomesgenefilter-1.64.0 genefilter: methods for filtering genes from high-throughput experimentsgeneplotter-1.60.0 Graphics related functions for Bioconductorgenerics-0.0.2 Common S3 Generics not Provided by Base R Methods Related to
Model Fittinggenoset-1.38.0 A RangedSummarizedExperiment with methods for copy number analysisgeometry-0.3-6 Mesh Generation and Surface Tessellationgetopt-1.20.2 C-Like ‘getopt’ BehaviorggExtra-0.8 Add Marginal Histograms to ‘ggplot2’, and More ‘ggplot2’
Enhancementsggbeeswarm-0.6.0 Categorical Scatter (Violin Point) Plotsggbio-1.30.0 Visualization tools for genomic dataggforce-0.1.3 Accelerating ‘ggplot2’ggm-2.3 Functions for graphical Markov modelsggplot2-3.1.0 Create Elegant Data Visualisations Using the Grammar of Graphicsggraph-1.0.2 An Implementation of Grammar of Graphics for Graphs and Networksggrepel-0.8.0 Automatically Position Non-Overlapping Text Labels with
‘ggplot2’ggridges-0.5.1 Ridgeline Plots in ‘ggplot2’ggthemes-4.1.0 Extra Themes, Scales and Geoms for ‘ggplot2’ggtree-1.14.6 an R package for visualization and annotation of phylogenetic trees with their covariates and other associated dataggvis-0.4.4 Interactive Grammar of Graphicsgh-1.0.1 ‘GitHub’ ‘API’git2r-0.23.0 Provides Access to Git Repositoriesglasso-1.10 Graphical Lasso: Estimation of Gaussian Graphical Modelsgllvm-1.1.0 Generalized Linear Latent Variable ModelsglmmML-1.0.3 Generalized Linear Models with ClusteringglmmTMB-0.2.2.0 Generalized Linear Mixed Models using Template Model Builderglmnet-2.0-16 Lasso and Elastic-Net Regularized Generalized Linear Modelsglmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox
Proportional Hazards Modelglobals-0.12.4 Identify Global Objects in R Expressionsglue-1.3.0 Interpreted String Literalsgmm-1.6-2 Generalized Method of Moments and Generalized Empirical
Likelihoodgmodels-2.18.1 Various R Programming Tools for Model Fittinggoftest-1.1-1 Classical Goodness-of-Fit Tests for Univariate Distributionsgomms-1.0 GLM-Based Ordination Methodgoseq-1.34.1 Gene Ontology analyser for RNA-seq and other length biased datagower-0.1.2 Gower’s Distancegplots-3.0.1 Various R Programming Tools for Plotting DatagrDevices built in
graph-1.60.0 graph: A package to handle graph data structuresgraphics built in
grid built in
gridBase-0.4-7 Integration of base and grid graphicsgridExtra-2.3 Miscellaneous Functions for “Grid” Graphicsgrpreg-3.2-0 Regularization Paths for Regression Models with Grouped
Covariatesgsalib-2.1 Utility Functions For GATKgsl-1.9-10.3 Wrapper for the Gnu Scientific Librarygsubfn-0.7 Utilities for Strings and Function Argumentsgsw-1.0-5 Gibbs Sea Water Functionsgtable-0.2.0 Arrange ‘Grobs’ in Tablesgtools-3.8.1 Various R Programming Toolsh2o-3.22.1.1 R Interface for ‘H2O’hapassoc-1.2-8 Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithmhaplo.stats-1.7.9 Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguoushaven-2.0.0 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Fileshdf5r-1.0.1 Interface to the ‘HDF5’ Binary Data Formatheatmap3-1.1.1 An Improved Heatmap Packagehexbin-1.27.2 Hexagonal Binning Routineshgu133plus2.db-3.2.3 Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2)highr-0.7 Syntax Highlighting for R Source Codehms-0.4.2 Pretty Time of Dayhopach-2.42.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)htmlTable-1.12 Advanced Tables for Markdown/HTMLhtmltools-0.3.6 Tools for HTMLhtmlwidgets-1.3 HTML Widgets for Rhttpcode-0.2.0 ‘HTTP’ Status Code Helperhttpuv-1.4.5.1 HTTP and WebSocket Server Libraryhttr-1.4.0 Tools for Working with URLs and HTTPhuge-1.2.7 High-Dimensional Undirected Graph Estimationhwriter-1.3.2 HTML Writer - Outputs R objects in HTML formatica-1.0-2 Independent Component Analysisidr-1.2 Irreproducible discovery rateigraph-1.2.2 Network Analysis and Visualizationigraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Packageilluminaio-0.24.0 Parsing Illumina Microarray Output Filesimager-0.41.1 Image Processing Library Based on ‘CImg’impute-1.56.0 impute: Imputation for microarray dataineq-0.2-13 Measuring Inequality, Concentration, and Povertyinferference-1.0.0 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-0.3.15 Functions to Inline C, C++, Fortran Function Calls from RinteractiveDisplayBase-1.20.0 Base package for enabling powerful shiny web displays of Bioconductor objectsinterpretR-0.2.4 Binary Classifier and Regression Model Interpretation Functionsinum-1.0-0 Interval and Enum-Type Representation of Vectorsipred-0.9-8 Improved Predictorsirace-3.1 Iterated Racing for Automatic Algorithm Configurationirlba-2.3.2 Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matricesiterators-1.0.10 Provides Iterator Construct for Ritertools-0.1-3 Iterator Toolsits-1.1.8 Irregular Time Seriesjomo-2.6-5 Multilevel Joint Modelling Multiple Imputationjpeg-0.1-8 Read and write JPEG imagesjsonlite-1.6 A Robust, High Performance JSON Parser and Generator for Rkernlab-0.9-27 Kernel-Based Machine Learning Labkin.cohort-0.7 Analysis of Kin-Cohort Studieskinship2-1.6.4 Pedigree FunctionsklaR-0.6-14 Classification and Visualizationknitr-1.21 A General-Purpose Package for Dynamic Report Generation in Rkohonen-3.0.8 Supervised and Unsupervised Self-Organising Mapsks-1.11.3 Kernel Smoothingkyotil-2018.10-17 Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studieslabdsv-1.8-0 Ordination and Multivariate Analysis for Ecologylabeling-0.3 Axis Labelinglabelled-2.0.1 Manipulating Labelled Datalaeken-0.4.6 Estimation of Indicators on Social Exclusion and Povertylambda.r-1.2.3 Modeling Data with Functional Programminglars-1.2 Least Angle Regression, Lasso and Forward Stagewiselasso2-1.2-20 L1 Constrained Estimation aka `lasso’latentnet-2.9.0 Latent Position and Cluster Models for Statistical Networkslater-0.7.5 Utilities for Delaying Function Executionlattice-0.20-38 Trellis Graphics for RlatticeExtra-0.6-28 Extra Graphical Utilities Based on Latticelava-1.6.4 Latent Variable Modelslavaan-0.6-3 Latent Variable Analysislazy-1.2-16 Lazy Learning for Local Regressionlazyeval-0.2.1 Lazy (Non-Standard) Evaluationleaps-3.0 Regression Subset Selectionlhs-0.16 Latin Hypercube Sampleslibcoin-1.0-2 Linear Test Statistics for Permutation InferencelimSolve-1.5.5.3 Solving Linear Inverse Modelslimma-3.38.3 Linear Models for Microarray Datalintr-1.0.3 A ‘Linter’ for R CodeliquidSVM-1.2.2 A Fast and Versatile SVM Packagelistenv-0.7.0 Environments Behaving (Almost) as Listslme4-1.1-19 Linear Mixed-Effects Models using ‘Eigen’ and S4lmtest-0.9-36 Testing Linear Regression Modelslocfdr-1.1-8 Computes Local False Discovery Rateslocfit-1.5-9.1 Local Regression, Likelihood and Density Estimation.logcondens-2.1.5 Estimate a Log-Concave Probability Density from Iid Observationslogistf-1.23 Firth’s Bias-Reduced Logistic Regressionlogspline-2.1.11 Routines for Logspline Density Estimationlokern-1.1-8 Kernel Regression Smoothing with Local or Global Plug-in
Bandwidthlongitudinal-1.1.12 Analysis of Multiple Time Course Datalongmemo-1.1-1 Statistics for Long-Memory Processes (Book Jan Beran), and
Related FunctionalitylpSolve-5.6.13 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programslpridge-1.0-8 Local Polynomial (Ridge) Regressionlqa-1.0-3 Penalized Likelihood Inference for GLMslsei-1.2-0 Solving Least Squares or Quadratic Programming Problems under
Equality/Inequality Constraintslubridate-1.7.4 Make Dealing with Dates a Little Easierlumi-2.34.0 BeadArray Specific Methods for Illumina Methylation and Expression MicroarraysmaSigPro-1.54.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Datamagic-1.5-9 Create and Investigate Magic Squaresmagick-2.0 Advanced Graphics and Image-Processing in Rmagrittr-1.5 A Forward-Pipe Operator for RmanipulateWidget-0.10.0 Add Even More Interactivity to Interactive Chartsmapdata-2.3.0 Extra Map Databasesmapproj-1.2.6 Map Projectionsmaps-3.3.0 Draw Geographical Mapsmaptools-0.9-4 Tools for Handling Spatial Objectsmarkdown-0.9 Render Markdown with the C Library ‘Sundown’marray-1.60.0 Exploratory analysis for two-color spotted microarray datamatrixStats-0.54.0 Functions that Apply to Rows and Columns of Matrices (and to
Vectors)matrixcalc-1.0-3 Collection of functions for matrix calculationsmaxLik-1.3-4 Maximum Likelihood Estimation and Related Toolsmboost-2.9-1 Model-Based Boostingmclust-5.4.2 Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimationmcmc-0.9-5 Markov Chain Monte Carlomediation-4.4.6 Causal Mediation Analysismemoise-1.1.0 Memoisation of Functionsmemuse-4.0-0 Memory Estimation UtilitiesmetagenomeSeq-1.24.1 Statistical analysis for sparse high-throughput sequencingmetap-1.0 Meta-Analysis of Significance Valuesmethods built in
methylumi-2.28.0 Handle Illumina methylation datamgcv-1.8-26 Mixed GAM Computation Vehicle with Automatic Smoothness
Estimationmi-1.0 Missing Data Imputation and Model Checkingmice-3.4.0 Multivariate Imputation by Chained Equationsmime-0.6 Map Filenames to MIME Typesminfi-1.28.4 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-0.8-4 Miscellaneous 3D PlotsmiscTools-0.6-22 Miscellaneous Tools and UtilitiesmissForest-1.4 Nonparametric Missing Value Imputation using Random Forestmitml-0.3-6 Tools for Multiple Imputation in Multilevel ModelingmixOmics-6.6.2 Omics Data Integration Projectmixtools-1.1.0 Tools for Analyzing Finite Mixture Modelsmlbench-2.1-1 Machine Learning Benchmark Problemsmlegp-3.1.7 Maximum Likelihood Estimates of Gaussian Processesmlogit-0.3-0 Multinomial Logit Modelsmlr-2.13 Machine Learning in Rmltools-0.3.5 Machine Learning Toolsmnormt-1.5-5 The Multivariate Normal and t Distributionsmodelr-0.1.2 Modelling Functions that Work with the Pipemodeltools-0.2-22 Tools and Classes for Statistical Modelsmoments-0.14 Moments, cumulants, skewness, kurtosis and related testsmondate-0.10.01.02 Keep track of dates in terms of monthsmpath-0.3-5 Regularized Linear Modelsmsm-1.6.6 Multi-State Markov and Hidden Markov Models in Continuous Timemultcomp-1.4-8 Simultaneous Inference in General Parametric Modelsmulticool-0.1-10 Permutations of Multisets in Cool-Lex Ordermulttest-2.38.0 Resampling-based multiple hypothesis testingmunsell-0.5.0 Utilities for Using Munsell Coloursmvabund-3.13.1 Statistical Methods for Analysing Multivariate Abundance Datamvtnorm-1.0-8 Multivariate Normal and t Distributionsnatserv-0.1.4 ‘NatureServe’ Interfacencbit-2013.03.29 retrieve and build NBCI taxonomic datancdf4-1.16.1 Interface to Unidata netCDF (Version 4 or Earlier) Format Data
FilesncdfFlow-2.28.1 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.network-1.13.0.1 Classes for Relational DatanetworkDynamic-0.9.0 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 Datanleqslv-3.3.2 Solve Systems of Nonlinear Equationsnlme-3.1-137 Linear and Nonlinear Mixed Effects Modelsnloptr-1.2.1 R Interface to NLoptnnet-7.3-12 Feed-Forward Neural Networks and Multinomial Log-Linear Modelsnnls-1.4 The Lawson-Hanson algorithm for non-negative least squares<U+000a>(NNLS)nor1mix-1.2-3 Normal aka Gaussian (1-d) Mixture Models (S3 Classes and
Methods)np-0.60-9 Nonparametric Kernel Smoothing Methods for Mixed Data Typesnpsurv-0.4-0 Nonparametric Survival AnalysisnumDeriv-2016.8-1 Accurate Numerical Derivativesnws-1.7.0.1 R functions for NetWorkSpaces and Sleighoce-1.0-1 Analysis of Oceanographic Dataoddsratio-1.0.3 Odds Ratio Calculation for GAM(M)s & GLM(M)soligoClasses-1.44.0 Classes for high-throughput arrays supported by oligo and crlmmopenCyto-1.20.2 Hierarchical Gating Pipeline for flow cytometry dataopenssl-1.1 Toolkit for Encryption, Signatures and Certificates Based on
OpenSSLopenxlsx-4.1.0 Read, Write and Edit XLSX Filesoptmatch-0.9-10 Functions for Optimal Matchingoptparse-1.6.0 Command Line Option Parserordinal-2018.8-25 Regression Models for Ordinal Dataorg.Hs.eg.db-3.7.0 Genome wide annotation for HumanpROC-1.13.0 Display and Analyze ROC Curvespackrat-0.5.0 A Dependency Management System for Projects and their R Package
Dependenciespan-1.6 Multiple Imputation for Multivariate Panel or Clustered DataparallelMap-1.3 Unified Interface to Parallelization Back-Endsparsedate-1.1.3 Recognize and Parse Dates in Various Formats, Including All ISO
8601 Formatspartools-1.1.6 Tools for the ‘Parallel’ Packageparty-1.3-1 A Laboratory for Recursive Partytioningpartykit-1.2-2 A Toolkit for Recursive Partytioningpastecs-1.3.21 Package for Analysis of Space-Time Ecological Seriespbapply-1.3-4 Adding Progress Bar to ‘*apply’ Functionspbivnorm-0.6.0 Vectorized Bivariate Normal CDFpbkrtest-0.4-7 Parametric Bootstrap and Kenward Roger Based Methods for Mixed
Model Comparisonpbs-1.1 Periodic B SplinespcaMethods-1.74.0 A collection of PCA methodspcaPP-1.9-73 Robust PCA by Projection Pursuitpdist-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-1.1-7 Parallelised Estimation of Prediction Errorperm-1.0-0.0 Exact or Asymptotic permutation testspermute-0.9-4 Functions for Generating Restricted Permutations of Dataphangorn-2.4.0 Phylogenetic Reconstruction and Analysispheatmap-1.0.10 Pretty Heatmapsphylobase-0.8.4 Base Package for Phylogenetic Structures and Comparative Datapillar-1.3.1 Coloured Formatting for Columnspim-2.0.1 Fit Probabilistic Index Modelspinfsc50-1.1.0 Sequence (‘FASTA’), Annotation (‘GFF’) and Variants (‘VCF’) for
17 Samples of ‘P. Infestans” and 1 ‘P. Mirabilis’pixmap-0.4-11 Bitmap Images (``Pixel Maps’’)pkgbuild-1.0.2 Find Tools Needed to Build R Packagespkgconfig-2.0.2 Private Configuration for ‘R’ Packagespkgload-1.0.2 Simulate Package Installation and Attachpkgmaker-0.27 Development Utilities for R Packagesplogr-0.2.0 The ‘plog’ C++ Logging Libraryplot3D-1.1.1 Plotting Multi-Dimensional Dataplot3Drgl-1.0.1 Plotting Multi-Dimensional Data - Using ‘rgl’plotly-4.8.0 Create Interactive Web Graphics via ‘plotly.js’plotrix-3.7-4 Various Plotting Functionspls-2.7-0 Partial Least Squares and Principal Component Regressionplyr-1.8.4 Tools for Splitting, Applying and Combining Datapng-0.1-7 Read and write PNG imagespolspline-1.1.13 Polynomial Spline Routinespolyclip-1.9-1 Polygon Clippingpolyester-1.18.0 Simulate RNA-seq readspolynom-1.3-9 A Collection of Functions to Implement a Class for Univariate
Polynomial Manipulationsprabclus-2.2-6 Functions for Clustering and Testing of Presence-Absence,
Abundance and Multilocus Genetic Datapracma-2.2.2 Practical Numerical Math Functionspraise-1.0.0 Praise UserspreprocessCore-1.44.0 A collection of pre-processing functionsprettyunits-1.0.2 Pretty, Human Readable Formatting of Quantitiesprocessx-3.2.1 Execute and Control System Processesprodlim-2018.04.18 Product-Limit Estimation for Censored Event History AnalysisprofileModel-0.5-9 Profiling Inference Functions for Various Model Classesprogress-1.2.0 Terminal Progress Barspromises-1.0.1 Abstractions for Promise-Based Asynchronous Programmingproto-1.0.0 Prototype Object-Based Programmingproxy-0.4-22 Distance and Similarity Measurespryr-0.1.4 Tools for Computing on the Languageps-1.3.0 List, Query, Manipulate System Processespscl-1.5.2 Political Science Computational Laboratorypspline-1.0-18 Penalized Smoothing Splinespsych-1.8.10 Procedures for Psychological, Psychometric, and Personality
Researchpsychotools-0.5-0 Psychometric Modeling Infrastructurepulsar-0.3.4 Parallel Utilities for Lambda Selection along a Regularization
Pathpurrr-0.2.5 Functional Programming Toolspvclust-2.0-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap
Resamplingqgraph-1.5 Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimationqpdf-1.1 Split, Combine and Compress PDF Filesqrnn-2.0.3 Quantile Regression Neural Networkqtl-1.44-9 Tools for Analyzing QTL Experimentsquadprog-1.5-5 Functions to Solve Quadratic Programming Problemsquantmod-0.4-13 Quantitative Financial Modelling Frameworkquantreg-5.38 Quantile Regressionquantsmooth-1.48.0 Quantile smoothing and genomic visualization of array dataquestionr-0.7.0 Functions to Make Surveys Processing Easierqvalue-2.14.1 Q-value estimation for false discovery rate controlqvcalc-0.9-1 Quasi Variances for Factor Effects in Statistical Modelsr2d3-0.2.3 Interface to ‘D3’ VisualizationsrARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD ProblemsrGADEM-2.30.0 de novo motif discoveryrJava-0.9-10 Low-Level R to Java InterfacerandomForest-4.6-14 Breiman and Cutler’s Random Forests for Classification and
RegressionrandomForestSRC-2.7.0 Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)ranger-0.10.1 A Fast Implementation of Random Forestsrappdirs-0.3.1 Application Directories: Determine Where to Save Data, Caches,
and Logsraster-2.8-4 Geographic Data Analysis and Modelingrbenchmark-1.0.0 Benchmarking routine for Rrcmdcheck-1.3.2 Run ‘R CMD check’ from ‘R’ and Capture Resultsreadbitmap-0.1.5 Simple Unified Interface to Read Bitmap Images
(BMP,JPEG,PNG,TIFF)readr-1.3.1 Read Rectangular Text Datareadxl-1.2.0 Read Excel Filesrecipes-0.1.4 Preprocessing Tools to Create Design Matricesrefund-0.1-17 Regression with Functional Dataregistry-0.5 Infrastructure for R Package Registriesregress-1.3-15 Gaussian Linear Models with Linear Covariance Structureregtools-1.0.1 Regression Toolsrelations-0.6-8 Data Structures and Algorithms for Relationsrelevent-1.0-4 Relational Event Modelsrematch-1.0.1 Match Regular Expressions with a Nicer ‘API’remotes-2.0.2 R Package Installation from Remote Repositories, Including
‘GitHub’rentrez-1.2.1 ‘Entrez’ in Rrepr-0.19.2 Serializable Representationsreprex-0.2.1 Prepare Reproducible Example Code via the Clipboardreshape-0.8.8 Flexibly Reshape Datareshape2-1.4.3 Flexibly Reshape Data: A Reboot of the Reshape Packagereticulate-1.10 Interface to ‘Python’rex-1.1.2 Friendly Regular Expressionsrgdal-1.3-6 Bindings for the ‘Geospatial’ Data Abstraction Libraryrgenoud-5.8-3.0 R Version of GENetic Optimization Using Derivativesrgexf-0.15.3 Build, Import and Export GEXF Graph Filesrgl-0.99.16 3D Visualization Using OpenGLrhdf5-2.26.2 HDF5 interface to Rrio-0.5.16 A Swiss-Army Knife for Data I/Oritis-0.7.6 Integrated Taxonomic Information System Clientrjags-4-8 Bayesian Graphical Models using MCMCrjson-0.2.20 JSON for Rrlang-0.3.2 Functions for Base Types and Core R and ‘Tidyverse’ Featuresrlecuyer-0.3-4 R Interface to RNG with Multiple Streamsrmarkdown-1.11 Dynamic Documents for Rrmeta-3.0 Meta-Analysisrms-5.1-2 Regression Modeling Strategiesrncl-0.8.3 An Interface to the Nexus Class Libraryrngtools-1.3.1 Utility Functions for Working with Random Number Generatorsrobustbase-0.93-3 Basic Robust StatisticsrootSolve-1.7 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of
Ordinary Differential Equationsrotl-3.0.5 Interface to the ‘Open Tree of Life’ APIroxygen2-6.1.1 In-Line Documentation for Rrpart-4.1-13 Recursive Partitioning and Regression Treesrprojroot-1.3-2 Finding Files in Project Subdirectoriesrrcov-1.4-7 Scalable Robust Estimators with High Breakdown Pointrredlist-0.5.0 ‘IUCN’ Red List Clientrsconnect-0.8.13 Deployment Interface for R Markdown Documents and Shiny
Applicationsrslurm-0.4.0 Submit R Calculations to a Slurm Clusterrstudioapi-0.8 Safely Access the RStudio APIrtracklayer-1.42.2 R interface to genome annotation files and the UCSC genome browserrvcheck-0.1.3 R/Package Version Checkrversions-1.0.3 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’rvest-0.3.2 Easily Harvest (Scrape) Web Pagesrzmq-0.9.6 R Bindings for ‘ZeroMQ’samr-3.0 SAM: Significance Analysis of Microarrayssandwich-2.5-0 Robust Covariance Matrix Estimatorsscales-1.0.0 Scale Functions for Visualizationscatterplot3d-0.3-41 3D Scatter Plotscidb-2.0.0 An R Interface to SciDBseewave-2.1.0 Sound Analysis and Synthesissegmented-0.5-3.0 Regression Models with Break-Points / Change-Points Estimationselectr-0.4-1 Translate CSS Selectors to XPath Expressionssem-3.1-9 Structural Equation ModelssendmailR-1.2-1 send email using RseqLogo-1.48.0 Sequence logos for DNA sequence alignmentsseqinr-3.4-5 Biological Sequences Retrieval and Analysissessioninfo-1.1.1 R Session Informationsets-1.0-18 Sets, Generalized Sets, Customizable Sets and Intervalssf-0.7-2 Simple Features for Rsfsmisc-1.1-3 Utilities from ‘Seminar fuer Statistik’ ETH Zurichshape-1.4.4 Functions for Plotting Graphical Shapes, Colorsshapefiles-0.7 Read and Write ESRI Shapefilesshiny-1.2.0 Web Application Framework for RshinyBS-0.61 Twitter Bootstrap Components for ShinyshinyFiles-0.7.2 A Server-Side File System Viewer for Shinyshinycssloaders-0.2.0 Add CSS Loading Animations to ‘shiny’ Outputsshinydashboard-0.7.1 Create Dashboards with ‘Shiny’shinyjs-1.0 Easily Improve the User Experience of Your Shiny Apps in Secondsshinythemes-1.1.2 Themes for ShinysigaR-1.30.0 Statistics for Integrative Genomics Analyses in Rsiggenes-1.56.0 Multiple testing using SAM and Efron’s empirical Bayes approachessignal-0.7-6 Signal Processingslam-0.1-44 Sparse Lightweight Arrays and Matricessm-2.2-5.6 Smoothing Methods for Nonparametric Regression and Density
Estimationsmoother-1.1 Functions Relating to the Smoothing of Numerical Datasn-1.5-3 The Skew-Normal and Related Distributions Such as the Skew-tsna-2.4 Tools for Social Network Analysissnow-0.4-3 Simple Network of Workstationssnowfall-1.84-6.1 Easier cluster computing (based on snow).snpStats-1.32.0 SnpMatrix and XSnpMatrix classes and methodssolrium-1.0.2 General Purpose R Interface to ‘Solr’som-0.3-5.1 Self-Organizing Mapsoundecology-1.3.3 Soundscape Ecologysourcetools-0.1.7 Tools for Reading, Tokenizing and Parsing R Codesp-1.3-1 Classes and Methods for Spatial DataspData-0.2.9.6 Datasets for Spatial Analysisspam-2.2-1 SPArse Matrixsparklyr-1.0.0 R Interface to Apache Sparkspatial-7.3-11 Functions for Kriging and Point Pattern Analysisspatstat-1.57-1 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Testsspatstat.data-1.4-0 Datasets for ‘spatstat’spatstat.utils-1.13-0 Utility Functions for ‘spatstat’spdep-0.8-1 Spatial Dependence: Weighting Schemes, Statistics and Modelssplines built in
sqldf-0.4-11 Manipulate R Data Frames Using SQLssgraph-1.7 Bayesian Graphical Estimation using Spike-and-Slab Priorsstabledist-0.7-1 Stable Distribution Functionsstabs-0.6-3 Stability Selection with Error Controlstartupmsg-0.9.5 Utilities for Start-Up Messagesstatmod-1.4.30 Statistical Modelingstatnet-2018.10 Software Tools for the Statistical Analysis of Network Datastatnet.common-4.1.4 Common R Scripts and Utilities Used by the Statnet Project
Softwarestats built in
stats4 built in
stringdist-0.9.5.1 Approximate String Matching and String Distance Functionsstringi-1.2.4 Character String Processing Facilitiesstringr-1.3.1 Simple, Consistent Wrappers for Common String Operationsstrucchange-1.5-1 Testing, Monitoring, and Dating Structural Changessubplex-1.5-4 Unconstrained Optimization using the Subplex Algorithmsurvey-3.35-1 Analysis of Complex Survey Samplessurvival-2.43-3 Survival AnalysissurvivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival datasvd-0.4.1 Interfaces to Various State-of-Art SVD and EigensolverssynapseClient 1.14-3
sys-3.1 Powerful and Reliable Tools for Running System Commands in RsystemPipeR-1.16.1 systemPipeR: NGS workflow and report generation environmenttables-0.8.7 Formula-Driven Table Generationtaxize-0.9.4 Taxonomic Information from Around the Webtclust-1.4-1 Robust Trimmed Clusteringtensor-1.5 Tensor product of arraystensorA-0.36.1 Advanced Tensor Arithmetic with Named Indicestergm-3.5.2 Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Modelstestthat-2.0.1 Unit Testing for Rtibble-1.4.2 Simple Data Framestidygraph-1.1.1 A Tidy API for Graph Manipulationtidyr-0.8.2 Easily Tidy Data with ‘spread()’ and ‘gather()’ Functionstidyselect-0.2.5 Select from a Set of Stringstidytree-0.2.4 A Tidy Tool for Phylogenetic Tree Data Manipulationtidyverse-1.2.1 Easily Install and Load the ‘Tidyverse’tiff-0.1-5 Read and write TIFF imagestilingArray-1.60.0 Transcript mapping with high-density oligonucleotide tiling arraystimeDate-3043.102 Rmetrics - Chronological and Calendar ObjectstimeSeries-3042.102 Rmetrics - Financial Time Series Objectstimereg-1.9.2 Flexible Regression Models for Survival Datatinytex-0.9 Helper Functions to Install and Maintain ‘TeX Live’, and Compile
‘LaTeX’ DocumentstkWidgets-1.60.0 R based tk widgetstkrplot-0.0-24 TK Rplottm-0.7-6 Text Mining Packagetmle-1.3.0-2 Targeted Maximum Likelihood Estimationtmvtnorm-1.4-10 Truncated Multivariate Normal and Student t Distributiontools built in
tree-1.0-39 Classification and Regression Treestreeio-1.6.2 Base Classes and Functions for Phylogenetic Tree Input and Outputtriebeard-0.3.0 ‘Radix’ Trees in ‘Rcpp’trimcluster-0.1-2.1 Cluster Analysis with Trimmingtripack-1.3-8 Triangulation of Irregularly Spaced Datatrust-0.1-7 Trust Region Optimizationtseries-0.10-46 Time Series Analysis and Computational FinancetseriesChaos-0.1-13 Analysis of Nonlinear Time Seriestsna-0.2.0 Tools for Temporal Social Network Analysistsne-0.1-3 T-Distributed Stochastic Neighbor Embedding for R (t-SNE)tuneR-1.3.3 Analysis of Music and Speechtweedie-2.3.2 Evaluation of Tweedie Exponential Family Modelstweenr-1.0.1 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-0.6-2 Measurement Units for R Vectorsurca-1.3-0 Unit Root and Cointegration Tests for Time Series Dataurltools-1.7.1 Vectorised Tools for URL Handling and Parsinguroot-2.0-9 Unit Root Tests for Seasonal Time Seriesusethis-1.4.0 Automate Package and Project Setuputf8-1.1.4 Unicode Text Processingutils built in
uuid-0.1-2 Tools for generating and handling of UUIDsvcd-1.4-4 Visualizing Categorical DatavcfR-1.8.0 Manipulate and Visualize VCF Datavegan-2.5-3 Community Ecology Packagevenn-1.7 Draw Venn Diagramsvioplot-0.2 Violin Plotvipor-0.4.5 Plot Categorical Data Using Quasirandom Noise and Density
Estimatesviridis-0.5.1 Default Color Maps from ‘matplotlib’viridisLite-0.3.0 Default Color Maps from ‘matplotlib’ (Lite Version)visNetwork-2.0.5 Network Visualization using ‘vis.js’ Libraryvsn-3.50.0 Variance stabilization and calibration for microarray datawaveslim-1.7.5 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-0.5.1 Take Screenshots of Web Pageswhisker-0.3-2 for R, logicless templatingwidgetTools-1.60.0 Creates an interactive tcltk widgetwikitaxa-0.3.0 Taxonomic Information from ‘Wikipedia’withr-2.1.2 Run Code ‘With’ Temporarily Modified Global Stateworrms-0.3.0 World Register of Marine Species (WoRMS) Clientxfun-0.4 Miscellaneous Functions by ‘Yihui Xie’xlsx-0.6.1 Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Filesxlsxjars-0.6.1 Package required POI jars for the xlsx packagexml2-1.2.0 Parse XMLxopen-1.0.0 Open System Files, ‘URLs’, Anythingxtable-1.8-3 Export Tables to LaTeX or HTMLxts-0.11-2 eXtensible Time Seriesyaml-2.2.0 Methods to Convert R Data to YAML and Backzip-1.0.0 Cross-Platform ‘zip’ Compressionzlibbioc-1.28.0 An R packaged zlib-1.2.5zoo-1.8-4 S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations)