Known Issues
Package List
ADGofTest-0.3 Anderson-Darling GoF testALDEx2-1.36.0 Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountALL-1.46.0 A data packageAgiMicroRna-2.54.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAnnotationDbi-1.66.0 Manipulation of SQLite-based annotations in BioconductorAnnotationFilter-1.28.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.46.0 Tools for building SQLite-based annotation data packagesAnnotationHub-3.12.0 Client to access AnnotationHub resourcesArchR 1.0.2 [CRAN]
BDgraph-2.72 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMCBH-1.84.0-0 Boost C++ Header FilesBSgenome-1.72.0 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)Bhat-0.9-12 General Likelihood ExplorationBiasedUrn-2.0.11 Biased Urn Model DistributionsBiobase-2.64.0 Biobase: Base functions for BioconductorBiocBaseUtils-1.6.0 General utility functions for developing Bioconductor packagesBiocFileCache-2.12.0 Manage Files Across SessionsBiocGenerics-0.50.0 S4 generic functions used in BioconductorBiocIO-1.14.0 Standard Input and Output for Bioconductor PackagesBiocManager-1.30.23 Access the Bioconductor Project Package RepositoryBiocNeighbors-1.22.0 Nearest Neighbor Detection for Bioconductor PackagesBiocParallel-1.38.0 Bioconductor facilities for parallel evaluationBiocSingular-1.20.0 Singular Value Decomposition for Bioconductor PackagesBiocStyle-2.32.0 Standard styles for vignettes and other Bioconductor documentsBiocVersion-3.19.1 Set the appropriate version of Bioconductor packagesBiostrings-2.72.0 Efficient manipulation of biological stringsBivarP-1.0 Estimating the Parameters of Some Bivariate DistributionsBolstad-0.2-41 Functions for Elementary Bayesian InferenceBolstad2-1.0-29 Bolstad FunctionsBradleyTerry2-1.1-2 Bradley-Terry ModelsCATALYST-1.28.0 Cytometry dATa anALYSis ToolsCGHbase-1.64.0 CGHbase: Base functions and classes for arrayCGH data analysis.CLONETv2-2.2.1 Clonality Estimates in TumorCMA-1.62.0 Synthesis of microarray-based classificationCNEr-1.40.0 CNE Detection and VisualizationCOMPASS-1.42.0 Combinatorial Polyfunctionality Analysis of Single CellsCVXR-1.0-12 Disciplined Convex OptimizationCairo-1.6-2 R Graphics Device using Cairo Graphics Library for Creating
High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG,
PostScript) and Display (X11 and Win32) OutputCategory-2.70.0 Category AnalysisChIPQC-1.40.0 Quality metrics for ChIPseq dataChIPpeakAnno-3.38.0 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval dataChIPseeker-1.40.0 ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationComplexHeatmap-2.20.0 Make Complex HeatmapsConsensusClusterPlus-1.68.0 ConsensusClusterPlusCytoML-2.16.0 A GatingML Interface for Cross Platform Cytometry Data SharingDAAG-1.25.4 Data Analysis and Graphics Data and FunctionsDECIPHER-3.0.0 Tools for curating, analyzing, and manipulating biological sequencesDEGseq-1.58.0 Identify Differentially Expressed Genes from RNA-seq dataDESeq2-1.44.0 Differential gene expression analysis based on the negative binomial distributionDEoptimR-1.1-3 Differential Evolution Optimization in Pure RDNAcopy-1.78.0 DNA Copy Number Data AnalysisDO.db-2.9 A set of annotation maps describing the entire Disease OntologyDOSE-3.30.0 Disease Ontology Semantic and Enrichment analysisDOT-0.1 Render and Export DOT Graphs in RDT-0.33 A Wrapper of the JavaScript Library ‘DataTables’DelayedArray-0.30.1 A unified framework for working transparently with on-disk and in-memory array-like datasetsDelayedMatrixStats-1.26.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ ObjectsDeriv-4.1.3 Symbolic DifferentiationDiffBind-3.14.0 Differential Binding Analysis of ChIP-Seq Peak DataDirichletMultinomial-1.46.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataDynDoc-1.82.0 Dynamic document toolsEBImage-4.46.0 Image processing and analysis toolbox for RECOSolveR-0.5.5 Embedded Conic Solver in REpiModel-2.4.0 Mathematical Modeling of Infectious Disease DynamicsExperimentHub-2.12.0 Client to access ExperimentHub resourcesFDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probesFNN-1.1.4 Fast Nearest Neighbor Search Algorithms and ApplicationsFlowSOM-2.12.0 Using self-organizing maps for visualization and interpretation of cytometry dataFormula-1.2-5 Extended Model FormulasGEOquery-2.72.0 Get data from NCBI Gene Expression Omnibus (GEO)GGally-2.2.1 Extension to ‘ggplot2’GO.db-3.19.1 A set of annotation maps describing the entire Gene OntologyGOSemSim-2.30.0 GO-terms Semantic Similarity MeasuresGOstats-2.70.0 Tools for manipulating GO and microarraysGSA-1.03.3 Gene Set AnalysisGSEABase-1.66.0 Gene set enrichment data structures and methodsGSVA-1.52.2 Gene Set Variation Analysis for Microarray and RNA-Seq DataGWASExactHW-1.2 Exact Hardy-Weinburg Testing for Genome Wide Association StudiesGWASTools-1.50.0 Tools for Genome Wide Association StudiesGenomeInfoDb-1.40.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming styleGenomeInfoDbData-1.2.12 Species and taxonomy ID look up tables used by GenomeInfoDbGenomicAlignments-1.40.0 Representation and manipulation of short genomic alignmentsGenomicFeatures-1.56.0 Conveniently import and query gene modelsGenomicFiles-1.40.0 Distributed computing by file or by rangeGenomicRanges-1.56.0 Representation and manipulation of genomic intervalsGetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable InterpolationGlimma-2.14.0 Interactive visualizations for gene expression analysisGlobalOptions-0.1.2 Generate Functions to Get or Set Global OptionsGmisc-3.0.3 Descriptive Statistics, Transition Plots, and MoreGreyListChIP-1.36.0 Grey Lists – Mask Artefact Regions Based on ChIP InputsGviz-1.48.0 Plotting data and annotation information along genomic coordinatesHDF5Array-1.32.0 HDF5 backend for DelayedArray objectsHDO.db-0.99.1 A set of annotation maps describing the entire Human Disease OntologyHMMcopy-1.46.0 Copy number prediction with correction for GC and mappability bias for HTS dataHSMMSingleCell-1.24.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)HaploSim-1.8.4.2 Functions to Simulate HaplotypesHmisc-5.1-2 Harrell MiscellaneousHomo.sapiens-1.3.1 Annotation package for the Homo.sapiens objectIDPmisc-1.1.21 ‘Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)’IHW-1.32.0 Independent Hypothesis WeightingIRanges-2.38.0 Foundation of integer range manipulation in BioconductorIRdisplay-1.1 ‘Jupyter’ Display MachineryIlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arraysInteractionSet-1.32.0 Base Classes for Storing Genomic Interaction DataKEGGREST-1.44.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)KEGGgraph-1.64.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorLogicReg-1.6.6 Logic RegressionLymphoSeq-1.32.0 Analyze high-throughput sequencing of T and B cell receptorsLymphoSeqDB-0.99.2 LymphoSeq annotation databasesMAGeCKFlute-2.8.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic ScreensMAST-1.30.0 Model-based Analysis of Single Cell TranscriptomicsMCMCglmm-2.36 MCMC Generalised Linear Mixed ModelsMPV-1.63 Data Sets from Montgomery, Peck and ViningMatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
OperationsMatrixExtra-0.1.15 Extra Methods for Sparse MatricesMatrixGenerics-1.16.0 S4 Generic Summary Statistic Functions that Operate on Matrix-Like ObjectsMatrixModels-0.5-3 Modelling with Sparse and Dense MatricesMfuzz-2.64.0 Soft clustering of time series gene expression dataNADA-1.6-1.1 Nondetects and Data Analysis for Environmental DataNOISeq-2.48.0 Exploratory analysis and differential expression for RNA-seq dataNozzle.R1-1.1-1.1 Nozzle ReportsOrganismDbi-1.46.0 Software to enable the smooth interfacing of different database packagesPBSddesolve-1.13.4 Solver for Delay Differential EquationsPFAM.db-3.19.1 A set of protein ID mappings for PFAMPICS-2.48.0 Probabilistic inference of ChIP-seqPolynomF-2.0-8 Polynomials in RProtGenerics-1.36.0 Generic infrastructure for Bioconductor mass spectrometry packagesQUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix EstimationQuickJSR-1.1.3 Interface for the ‘QuickJS’ Lightweight ‘JavaScript’ EngineR.methodsS3-1.8.2 S3 Methods SimplifiedR.oo-1.26.0 R Object-Oriented Programming with or without ReferencesR.utils-2.12.3 Various Programming UtilitiesR2WinBUGS-2.1-22.1 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’R2jags-0.8-5 Using R to Run ‘JAGS’RBGL-1.80.0 An interface to the BOOST graph libraryRCurl-1.98-1.14 General Network (HTTP/FTP/…) Client Interface for RREDCapR-1.1.0 Interaction Between R and REDCapRLRsim-3.1-8 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
ModelsRNASeqPower-1.44.0 Sample size for RNAseq studiesROCR-1.0-11 Visualizing the Performance of Scoring ClassifiersRPresto-1.4.6 DBI Connector to PrestoRProtoBuf-0.4.22 R Interface to the ‘Protocol Buffers’ ‘API’ (Version 2 or 3)RProtoBufLib-2.16.0 C++ headers and static libraries of Protocol buffersRSQLite-2.3.6 SQLite Interface for RRSclient-0.7-10 Client for RserveRSpectra-0.16-1 Solvers for Large-Scale Eigenvalue and SVD ProblemsRVenn-1.1.0 Set Operations for Many SetsRaggedExperiment-1.28.0 Representation of Sparse Experiments and Assays Across SamplesRcppAnnoy-0.0.22 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
NeighborsRcppArmadillo-0.12.8.3.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra
LibraryRcppCCTZ-0.2.12 ‘Rcpp’ Bindings for the ‘CCTZ’ LibraryRcppDate-0.0.3 ‘date’ C++ Header Library for Date and Time FunctionalityRcppEigen-0.3.4.0.0 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra
LibraryRcppGSL-0.3.13 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and MatricesRcppHNSW-0.6.0 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest
NeighborsRcppML-0.3.7 Rcpp Machine Learning LibraryRcppNumerical-0.6-0 ‘Rcpp’ Integration for Numerical Computing LibrariesRcppParallel-5.1.7 Parallel Programming Tools for ‘Rcpp’RcppProgress-0.4.2 An Interruptible Progress Bar with OpenMP Support for C++ in R
PackagesRcppTOML-0.2.2 ‘Rcpp’ Bindings to Parser for “Tom’s Obvious Markup Language”RcppThread-2.1.7 R-Friendly Threading in C++RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG
ImplementationsRdpack-2.6 Update and Manipulate Rd Documentation ObjectsRdsdp-1.0.5.2.1 R Interface to DSDP Semidefinite Programming LibraryReportingTools-2.44.0 Tools for making reports in various formatsRfast-2.1.0 A Collection of Efficient and Extremely Fast R FunctionsRgraphviz-2.48.0 Provides plotting capabilities for R graph objectsRhdf5lib-1.26.0 hdf5 library as an R packageRhpc-0.21-247 Permits *apply() Style Dispatch for ‘HPC’RhpcBLASctl-0.23-42 Control the Number of Threads on ‘BLAS’Rhtslib-3.0.0 HTSlib high-throughput sequencing library as an R packageRingo 1.66.0 [CRAN]
Rlabkey-3.2.1 Data Exchange Between R and ‘LabKey’ ServerRmpfr-0.9-5 R MPFR - Multiple Precision Floating-Point ReliableRmpi-0.7-2 Interface (Wrapper) to MPI (Message-Passing Interface)Rsamtools-2.20.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importRsubread-2.18.0 Mapping, quantification and variant analysis of sequencing dataRtsne-0.17 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
ImplementationS4Arrays-1.4.0 Foundation of array-like containers in BioconductorS4Vectors-0.42.0 Foundation of vector-like and list-like containers in BioconductorSNPRelate-1.38.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)SNPassoc-2.1-0 SNPs-Based Whole Genome Association StudiesSPIA-2.56.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsScaledMatrix-1.12.0 Creating a DelayedMatrix of Scaled and Centered ValuesSemiPar-1.0-4.2 Semiparametic RegressionShortRead-1.62.0 FASTQ input and manipulationSingleCellExperiment-1.26.0 S4 Classes for Single Cell DataSparseArray-1.4.3 High-performance sparse data representation and manipulation in RSparseM-1.81 Sparse Linear AlgebraSpatialExperiment-1.14.0 S4 Class for Spatially Resolved -omics DataStanHeaders-2.32.7 C++ Header Files for StanSummarizedExperiment-1.34.0 SummarizedExperiment containerSuperLearner-2.0-29 Super Learner PredictionTFBSTools-1.42.0 Software Package for Transcription Factor Binding Site (TFBS) AnalysisTFMPvalue-0.0.9 Efficient and Accurate P-Value Computation for Position Weight
MatricesTH.data-1.1-2 TH’s Data ArchiveTitanCNA-1.42.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumoursTxDb.Celegans.UCSC.ce6.ensGene-3.2.2 Annotation package for TxDb object(s)TxDb.Dmelanogaster.UCSC.dm3.ensGene-3.2.2 Annotation package for TxDb object(s)TxDb.Hsapiens.UCSC.hg18.knownGene-3.2.2 Annotation package for TxDb object(s)TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)TxDb.Mmusculus.UCSC.mm10.knownGene-3.10.0 Annotation package for TxDb object(s)TxDb.Mmusculus.UCSC.mm9.knownGene-3.2.2 Annotation package for TxDb object(s)TxDb.Rnorvegicus.UCSC.rn4.ensGene-3.2.2 Annotation package for TxDb object(s)UCSC.utils-1.0.0 Low-level utilities to retrieve data from the UCSC Genome BrowserUpSetR-1.4.0 A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting SetsV8-4.4.2 Embedded JavaScript and WebAssembly Engine for RVariantAnnotation-1.50.0 Annotation of Genetic VariantsVennDiagram-1.7.3 Generate High-Resolution Venn and Euler PlotsWrench-1.22.0 Wrench normalization for sparse count dataXML-3.99-0.16.1 Tools for Parsing and Generating XML Within R and S-PlusXVector-0.44.0 Foundation of external vector representation and manipulation in Bioconductorabind-1.4-5 Combine Multidimensional Arraysade4-1.7-22 Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciencesadmisc-0.35 Adrian Dusa’s Miscellaneousaffxparser-1.76.0 Affymetrix File Parsing SDKaffy-1.82.0 Methods for Affymetrix Oligonucleotide Arraysaffycoretools-1.76.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChipsaffyio-1.74.0 Tools for parsing Affymetrix data filesalr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Editionamap-0.8-19 Another Multidimensional Analysis Packageannaffy-1.76.0 Annotation tools for Affymetrix biological metadataannotate-1.82.0 Annotation for microarraysape-5.8 Analyses of Phylogenetics and Evolutionapeglm-1.26.0 Approximate posterior estimation for GLM coefficientsaplot-0.2.2 Decorate a ‘ggplot’ with Associated Informationargparser-0.7.2 Command-Line Argument Parserarsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical
Summariesarules-1.7-7 Mining Association Rules and Frequent Itemsetsash-1.0-15 David Scott’s ASH Routinesashr-2.2-63 Methods for Adaptive Shrinkage, using Empirical Bayesassertthat-0.2.1 Easy Pre and Post Assertionsaws.ec2metadata-0.2.0 Get EC2 Instance Metadataaws.s3-0.3.21 ‘AWS S3’ Client Packageaws.signature-0.6.0 Amazon Web Services Request Signaturesbabelgene-22.9 Gene Orthologs for Model Organisms in a Tidy Data Formatbamsignals-1.36.0 Extract read count signals from bam filesbase64-2.0.1 Base64 Encoder and Decoderbase64url-1.4 Fast and URL-Safe Base64 Encoder and Decoderbasilisk-1.16.0 Freezing Python Dependencies Inside Bioconductor Packagesbasilisk.utils-1.16.0 Basilisk Installation Utilitiesbatchtools-0.9.17 Tools for Computation on Batch Systemsbayesplot-1.11.1 Plotting for Bayesian Modelsbbmle-1.0.25.1 Tools for General Maximum Likelihood Estimationbdsmatrix-1.3-7 Routines for Block Diagonal Symmetric Matricesbeachmat-2.20.0 Compiling Bioconductor to Handle Each Matrix Typebeanplot-1.3.1 Visualization via Beanplots (Like Boxplot/Stripchart/Violin
Plot)beeswarm-0.4.0 The Bee Swarm Plot, an Alternative to Stripchartbenchmark-0.3-6 Benchmark Experiments Toolboxbezier-1.1.2 Toolkit for Bezier Curves and Splinesbiglm-0.9-2.1 Bounded Memory Linear and Generalized Linear ModelsbiomaRt-2.60.0 Interface to BioMart databases (i.e. Ensembl)biomformat-1.32.0 An interface package for the BIOM file formatbiovizBase-1.52.0 Basic graphic utilities for visualization of genomic data.bitops-1.0-7 Bitwise Operationsbookdown-0.39 Authoring Books and Technical Documents with R Markdownboot-1.3-30 Bootstrap Functions (Originally by Angelo Canty for S)breakaway-4.8.4 Species Richness Estimation and Modelingbrglm-0.7.2 Bias Reduction in Binomial-Response Generalized Linear Modelsbroom.helpers-1.15.0 Helpers for Model Coefficients Tibblesbumphunter-1.46.0 Bump HuntercaTools-1.18.2 Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etccar-3.1-2 Companion to Applied RegressioncarData-3.0-5 Companion to Applied Regression Data Setscatdata-1.2.4 Categorical Datacheckmate-2.3.1 Fast and Versatile Argument Checkschipseq-1.54.0 chipseq: A package for analyzing chipseq datachromVAR-1.26.0 Chromatin Variation Across Regionschron-2.3-61 Chronological Objects which Can Handle Dates and Timescirclize-0.4.16 Circular VisualizationclassInt-0.4-10 Choose Univariate Class Intervalsclue-0.3-65 Cluster Ensemblescluster-2.1.6 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et
al.clusterProfiler-4.12.0 A universal enrichment tool for interpreting omics datacoda-0.19-4.1 Output Analysis and Diagnostics for MCMCcolorRamps-2.3.4 Builds Color Tablescolourpicker-1.3.0 A Colour Picker Tool for Shiny and for Selecting Colours in
Plotscompare-0.2-6 Comparing Objects for Differencesconfig-0.3.2 Manage Environment Specific Configuration Valuescopula-1.1-3 Multivariate Dependence with Copulascorpcor-1.6.10 Efficient Estimation of Covariance and (Partial) Correlationcorrplot-0.92 Visualization of a Correlation Matrixcowplot-1.1.3 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’crosstalk-1.2.1 Inter-Widget Interactivity for HTML Widgetscrul-1.4.2 HTTP Clientcubature-2.1.0 Adaptive Multivariate Integration over HypercubescummeRbund-2.46.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.curry-0.1.1 Partial Function Application with %<%, %-<%, and %><%cvAUC-1.1.4 Cross-Validated Area Under the ROC Curve Confidence Intervalscyclocomp-1.1.1 Cyclomatic Complexity of R Codecytolib-2.16.0 C++ infrastructure for representing and interacting with the gated cytometry datadada2-1.32.0 Accurate, high-resolution sample inference from amplicon sequencing datadbscan-1.1-12 Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related AlgorithmsdeSolve-1.40 Solvers for Initial Value Problems of Differential Equations
(‘ODE’, ‘DAE’, ‘DDE’)degreenet-1.3-5 Models for Skewed Count Distributions Relevant to Networksdeldir-2.0-4 Delaunay Triangulation and Dirichlet (Voronoi) Tessellationdensvis-1.14.0 Density-Preserving Data Visualization via Non-Linear Dimensionality Reductiondepmap-1.18.0 Cancer Dependency Map Data Packagederfinder-1.38.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approachderfinderHelper-1.38.0 derfinder helper packagedescr-1.1.8 Descriptive Statisticsdfoptim-2023.1.0 Derivative-Free Optimizationdiamonds-1.0-5 Analysis and sampling grids from diamond partitionsdichromat-2.0-0.1 Color Schemes for DichromatsdiffusionMap-1.2.0 Diffusion Mapdir.expiry-1.12.0 Managing Expiration for Cache Directoriesdirectlabels-2024.1.21 Direct Labels for Multicolor Plotsdistributional-0.4.0 Vectorised Probability DistributionsdoBy-4.6.21 Groupwise Statistics, LSmeans, Linear Estimates, UtilitiesdoMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi PackagedoParallel-1.0.17 Foreach Parallel Adaptor for the ‘parallel’ PackagedoRNG-1.8.6 Generic Reproducible Parallel Backend for ‘foreach’ Loopsdownloader-0.4 Download Files over HTTP and HTTPSdqrng-0.4.0 Fast Pseudo Random Number Generatorsdrc-3.0-1 Analysis of Dose-Response Curvesdygraphs-1.1.1.6 Interface to ‘Dygraphs’ Interactive Time Series Charting Librarye1071-1.7-14 Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU WienedgeR-4.2.0 Empirical Analysis of Digital Gene Expression Data in Regor-1.24.2 Import and Analyse Ego-Centered Network Dataelasticnet-1.3 Elastic-Net for Sparse Estimation and Sparse PCAellipse-0.5.0 Functions for Drawing Ellipses and Ellipse-Like Confidence
Regionsemdbook-1.3.13 Support Functions and Data for “Ecological Models and Data”enrichplot-1.24.0 Visualization of Functional Enrichment Resultensembldb-2.28.0 Utilities to create and use Ensembl-based annotation databasesepitools-0.5-10.1 Epidemiology Toolsergm-4.6.0 Fit, Simulate and Diagnose Exponential-Family Models for
Networksergm.ego-1.1.0 Fit, Simulate and Diagnose Exponential-Family Random Graph
Models to Egocentrically Sampled Network Dataergm.multi-0.2.1 Fit, Simulate and Diagnose Exponential-Family Models for
Multiple or Multilayer Networksetrunct-0.1 Computes Moments of Univariate Truncated t Distributioneuropepmc-0.4.3 R Interface to the Europe PubMed Central RESTful Web ServicefANCOVA-0.6-1 Nonparametric Analysis of Covariancefaraway-1.0.8 Functions and Datasets for Books by Julian Farawayfastcluster-1.2.6 Fast Hierarchical Clustering Routines for R and ‘Python’fastmatch-1.1-4 Fast ‘match()’ Functionfastseg-1.50.0 fastseg - a fast segmentation algorithmfasttime-1.1-0 Fast Utility Function for Time Parsing and Conversionfda-6.1.8 Functional Data Analysisfdrtool-1.2.17 Estimation of (Local) False Discovery Rates and Higher Criticismfds-1.8 Functional Data Setsff-4.0.12 Memory-Efficient Storage of Large Data on Disk and Fast Access
Functionsfftwtools-0.9-11 Wrapper for ‘FFTW3’ Includes: One-Dimensional, Two-Dimensional,
Three-Dimensional, and Multivariate Transformsfgsea-1.30.0 Fast Gene Set Enrichment Analysisfilelock-1.0.3 Portable File Lockingfit.models-0.64 Compare Fitted Modelsfloat-0.3-2 32-Bit FloatsflowClust-3.42.0 Clustering for Flow CytometryflowCore-2.16.0 flowCore: Basic structures for flow cytometry dataflowStats-4.16.0 Statistical methods for the analysis of flow cytometry dataflowViz-1.68.0 Visualization for flow cytometryflowWorkspace-4.16.0 Infrastructure for representing and interacting with gated and ungated cytometry data sets.fontBitstreamVera-0.1.1 Fonts with ‘Bitstream Vera Fonts’ LicensefontLiberation-0.1.0 Liberation Fontsfontquiver-0.2.1 Set of Installed Fontsforeign-0.8-86 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’,
‘Systat’, ‘Weka’, ‘dBase’, …forestplot-3.1.3 Advanced Forest Plot Using ‘grid’ Graphicsforge-0.2.0 Casting Values into ShapeformatR-1.14 Format R Code Automaticallyformula.tools-1.7.1 Programmatic Utilities for Manipulating Formulas, Expressions,
Calls, Assignments and Other R Objectsfts-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 Managementgage-2.54.0 Generally Applicable Gene-set Enrichment for Pathway Analysisgam-1.22-3 Generalized Additive Modelsgamm4-0.2-6 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’gcrma-2.76.0 Background Adjustment Using Sequence Informationgdsfmt-1.40.0 gdtools-0.3.7 Utilities for Graphical Rendering and Fonts ManagementgeneLenDataBase-1.39.0 Lengths of mRNA transcripts for a number of genomesgenefilter-1.86.0 genefilter: methods for filtering genes from high-throughput experimentsgeneplotter-1.82.0 Graphics related functions for Bioconductorgfonts-0.2.0 Offline ‘Google’ Fonts for ‘Markdown’ and ‘Shiny’ggVennDiagram-1.5.2 A ‘ggplot2’ Implement of Venn Diagramggbeeswarm-0.7.2 Categorical Scatter (Violin Point) Plotsggbio-1.52.0 Visualization tools for genomic dataggcyto-1.32.0 Visualize Cytometry data with ggplotggdendro-0.2.0 Create Dendrograms and Tree Diagrams Using ‘ggplot2’ggforce-0.4.2 Accelerating ‘ggplot2’ggfun-0.1.4 Miscellaneous Functions for ‘ggplot2’ggnewscale-0.4.10 Multiple Fill and Colour Scales in ‘ggplot2’ggplotify-0.1.2 Convert Plot to ‘grob’ or ‘ggplot’ Objectggpointdensity-0.1.0 A Cross Between a 2D Density Plot and a Scatter Plotggpubr-0.6.0 ‘ggplot2’ Based Publication Ready Plotsggraph-2.2.1 An Implementation of Grammar of Graphics for Graphs and Networksggrastr-1.0.2 Rasterize Layers for ‘ggplot2’ggrepel-0.9.5 Automatically Position Non-Overlapping Text Labels with
‘ggplot2’ggridges-0.5.6 Ridgeline Plots in ‘ggplot2’ggsci-3.0.3 Scientific Journal and Sci-Fi Themed Color Palettes for
‘ggplot2’ggsignif-0.6.4 Significance Brackets for ‘ggplot2’ggstats-0.6.0 Extension to ‘ggplot2’ for Plotting Statsggthemes-5.1.0 Extra Themes, Scales and Geoms for ‘ggplot2’ggtree-3.12.0 an R package for visualization of tree and annotation dataglmnet-4.1-8 Lasso and Elastic-Net Regularized Generalized Linear Modelsglmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox
Proportional Hazards Modelgmp-0.7-4 Multiple Precision Arithmeticgoftest-1.2-3 Classical Goodness-of-Fit Tests for Univariate Distributionsgplots-3.1.3.1 Various R Programming Tools for Plotting Datagraph-1.82.0 graph: A package to handle graph data structuresgraphlayouts-1.1.1 Additional Layout Algorithms for Network VisualizationsgridExtra-2.3 Miscellaneous Functions for “Grid” GraphicsgridGraphics-0.5-1 Redraw Base Graphics Using ‘grid’ Graphicsgrpreg-3.4.0 Regularization Paths for Regression Models with Grouped
Covariatesgsl-2.1-8 Wrapper for the Gnu Scientific Librarygson-0.1.0 Base Class and Methods for ‘gson’ Formatgsubfn-0.7 Utilities for Strings and Function Argumentsgtools-3.9.5 Various R Programming Toolshapassoc-1.2-9 Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithmhaplo.stats-1.9.5.1 Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguoushdrcde-3.4 Highest Density Regions and Conditional Density Estimationhere-1.0.1 A Simpler Way to Find Your Fileshexbin-1.28.3 Hexagonal Binning Routineshgu133plus2.db-3.13.0 Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)hopach-2.64.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)htmlTable-2.4.2 Advanced Tables for Markdown/HTMLhttpcode-0.3.0 ‘HTTP’ Status Code Helperhwriter-1.3.2.1 HTML Writer - Outputs R Objects in HTML Formathypergate-0.8.5 Machine Learning of Hyperrectangular Gating Strategies for
High-Dimensional Cytometryigraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Packageilluminaio-0.46.0 Parsing Illumina Microarray Output Filesimpute-1.78.0 impute: Imputation for microarray dataineq-0.2-13 Measuring Inequality, Concentration, and Povertyinferference-1.0.2 Methods for Causal Inference with Interferenceinline-0.3.19 Functions to Inline C, C++, Fortran Function Calls from RinteractiveDisplayBase-1.42.0 Base package for enabling powerful shiny web displays of Bioconductor objectsinterp-1.1-6 Interpolation Methodsinvgamma-1.1 The Inverse Gamma Distributioniotools-0.3-5 I/O Tools for Streamingirlba-2.3.5.1 Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matricesits-1.1.8 Irregular Time Seriesjomo-2.7-6 Multilevel Joint Modelling Multiple Imputationjpeg-0.1-10 Read and write JPEG imageskaryoploteR-1.30.0 Plot customizable linear genomes displaying arbitrary datakernlab-0.9-32 Kernel-Based Machine Learning Labkeyring-1.3.2 Access the System Credential Store from Rkin.cohort-0.7 Analysis of Kin-Cohort Studiesknockoff-0.3.6 The Knockoff Filter for Controlled Variable Selectionks-1.14.2 Kernel Smoothingkyotil-2024.5-8 Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studieslabelled-2.13.0 Manipulating Labelled Datalambda.r-1.2.4 Modeling Data with Functional Programminglars-1.3 Least Angle Regression, Lasso and Forward Stagewiselatentnet-2.11.0 Latent Position and Cluster Models for Statistical NetworkslatticeExtra-0.6-30 Extra Graphical Utilities Based on Latticelazyeval-0.2.2 Lazy (Non-Standard) Evaluationlgr-0.4.4 A Fully Featured Logging Frameworklimma-3.60.0 Linear Models for Microarray Datalintr-3.1.2 A ‘Linter’ for R Codelme4-1.1-35.3 Linear Mixed-Effects Models using ‘Eigen’ and S4lmtest-0.9-40 Testing Linear Regression Modelslocfit-1.5-9.9 Local Regression, Likelihood and Density Estimationlogistf-1.26.0 Firth’s Bias-Reduced Logistic Regressionlogspline-2.1.22 Routines for Logspline Density Estimationlokern-1.1-11 Kernel Regression Smoothing with Local or Global Plug-in
Bandwidthloo-2.7.0 Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
ModelslpSolveAPI-5.5.2.0-17.11 R Interface to ‘lp_solve’ Version 5.5.2.0lpridge-1.1-0 Local Polynomial (Ridge) Regressionlpsymphony-1.32.0 Symphony integer linear programming solver in Rlumi-2.56.0 BeadArray Specific Methods for Illumina Methylation and Expression MicroarraysmaSigPro-1.76.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Datamagic-1.6-1 Create and Investigate Magic Squaresmagick-2.8.3 Advanced Graphics and Image-Processing in Rmapdata-2.3.1 Extra Map Databasesmaps-3.4.2 Draw Geographical Mapsmarkdown-1.12 Render Markdown with ‘commonmark’marray-1.82.0 Exploratory analysis for two-color spotted microarray datamatrixStats-1.3.0 Functions that Apply to Rows and Columns of Matrices (and to
Vectors)mclust-6.1.1 Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density EstimationmetagenomeSeq-1.46.0 Statistical analysis for sparse high-throughput sequencingmethylKit-1.30.0 DNA methylation analysis from high-throughput bisulfite sequencing resultsmethylumi-2.50.0 Handle Illumina methylation datamice-3.16.0 Multivariate Imputation by Chained Equationsmicrobenchmark-1.4.10 Accurate Timing Functionsminfi-1.50.0 Analyze Illumina Infinium DNA methylation arraysminqa-1.2.6 Derivative-Free Optimization Algorithms by Quadratic
Approximationmisc3d-0.9-1 Miscellaneous 3D Plotsmitml-0.4-5 Tools for Multiple Imputation in Multilevel Modelingmitools-2.4 Tools for Multiple Imputation of Missing DatamixOmics-6.28.0 Omics Data Integration Projectmixsqp-0.3-54 Sequential Quadratic Programming for Fast Maximum-Likelihood
Estimation of Mixture Proportionsmlapi-0.1.1 Abstract Classes for Building ‘scikit-learn’ Like APImnormt-2.1.1 The Multivariate Normal and t Distributions, and Their Truncated
Versionsmondate-1.0 Keep Track of Dates in Terms of Monthsmotifmatchr-1.26.0 Fast Motif Matching in Rmsa-1.36.0 Multiple Sequence Alignmentmsigdbr-7.5.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Formatmultcomp-1.4-25 Simultaneous Inference in General Parametric Modelsmulticool-1.0.1 Permutations of Multisets in Cool-Lex Ordermulttest-2.60.0 Resampling-based multiple hypothesis testingmvtnorm-1.2-4 Multivariate Normal and t Distributionsnabor-0.5.0 Wraps ‘libnabo’, a Fast K Nearest Neighbour Library for Low
Dimensionsnanotime-0.3.7 Nanosecond-Resolution Time Support for RncdfFlow-2.50.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.network-1.18.2 Classes for Relational DatanetworkDynamic-0.11.4 Dynamic Extensions for Network ObjectsnetworkLite-1.0.5 An Simplified Implementation of the ‘network’ Package
Functionalitynetworksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through
Sequential Importance Samplingnleqslv-3.3.5 Solve Systems of Nonlinear Equationsnloptr-2.0.3 R Interface to NLoptnnls-1.5 The Lawson-Hanson Algorithm for Non-Negative Least Squares
(NNLS)nor1mix-1.3-3 Normal aka Gaussian 1-d Mixture Modelsnumbers-0.8-5 Number-Theoretic Functionsnws-1.7.0.1 R functions for NetWorkSpaces and Sleighodbc-1.4.2 Connect to ODBC Compatible Databases (using the DBI Interface)oligo-1.68.0 Preprocessing tools for oligonucleotide arraysoligoClasses-1.66.0 Classes for high-throughput arrays supported by oligo and crlmmopenCyto-2.16.0 Hierarchical Gating Pipeline for flow cytometry dataopenxlsx-4.2.5.2 Read, Write and Edit xlsx Filesoperator.tools-1.6.3 Utilities for Working with R’s Operatorsordinal-2023.12-4 Regression Models for Ordinal Dataorg.Hs.eg.db-3.19.1 Genome wide annotation for Humanorg.Mm.eg.db-3.19.1 Genome wide annotation for Mouseosqp-0.6.3.2 Quadratic Programming Solver using the ‘OSQP’ LibrarypROC-1.18.5 Display and Analyze ROC Curvespack-0.1-1 Convert values to/from raw vectorspan-1.9 Multiple Imputation for Multivariate Panel or Clustered Datapartools-1.1.6 Tools for the ‘Parallel’ Packagepathview-1.44.0 a tool set for pathway based data integration and visualizationpbapply-1.7-2 Adding Progress Bar to ‘*apply’ Functionspbkrtest-0.5.2 Parametric Bootstrap, Kenward-Roger and Satterthwaite Based
Methods for Test in Mixed Modelspbs-1.1 Periodic B SplinespcaMethods-1.96.0 A collection of PCA methodspcaPP-2.0-4 Robust PCA by Projection Pursuitpdftools-3.4.0 Text Extraction, Rendering and Converting of PDF Documentspdist-1.2.1 Partitioned Distance Functionpedigree-1.4.2 Pedigree Functionspedigreemm-0.3-4 Pedigree-Based Mixed-Effects Modelsperm-1.0-0.4 Exact or Asymptotic Permutation Testspermute-0.9-7 Functions for Generating Restricted Permutations of Dataphangorn-2.11.1 Phylogenetic Reconstruction and Analysispheatmap-1.0.12 Pretty Heatmapsphyloseq-1.48.0 Handling and analysis of high-throughput microbiome census datapixmap-0.4-13 Bitmap Images / Pixel Mapsplogr-0.2.0 The ‘plog’ C++ Logging Libraryplot3D-1.4.1 Plotting Multi-Dimensional Dataplotly-4.10.4 Create Interactive Web Graphics via ‘plotly.js’plotrix-3.8-4 Various Plotting Functionsplyr-1.8.9 Tools for Splitting, Applying and Combining Datapng-0.1-8 Read and write PNG imagespoisbinom-1.0.1 A Faster Implementation of the Poisson-Binomial Distributionpolspline-1.1.25 Polynomial Spline Routinespolyclip-1.10-6 Polygon Clippingpolyester-1.39.0 Simulate RNA-seq readspolynom-1.4-1 A Collection of Functions to Implement a Class for Univariate
Polynomial Manipulationspolyreg-0.8.0 Polynomial Regressionposterior-1.5.0 Tools for Working with Posterior DistributionspoweRlaw-0.80.0 Analysis of Heavy Tailed Distributionspracma-2.4.4 Practical Numerical Math Functionspremessa 0.3.4 [CRAN]
preprocessCore-1.66.0 A collection of pre-processing functionsprofileModel-0.6.1 Profiling Inference Functions for Various Model Classesproto-1.0.0 Prototype Object-Based Programmingproxy-0.4-27 Distance and Similarity Measurespspline-1.0-19 Penalized Smoothing Splinespsychotools-0.7-4 Psychometric Modeling Infrastructurepwalign-1.0.0 Perform pairwise sequence alignmentsqdapRegex-0.7.8 Regular Expression Removal, Extraction, and Replacement Toolsqpdf-1.3.3 Split, Combine and Compress PDF Filesqqconf-1.3.2 Creates Simultaneous Testing Bands for QQ-Plotsqtl-1.66 Tools for Analyzing QTL Experimentsquadprog-1.5-8 Functions to Solve Quadratic Programming Problemsquantoptr-0.1.3 Algorithms for Quantile- And Mean-Optimal Treatment Regimesquantreg-5.97 Quantile Regressionquantsmooth-1.70.0 Quantile smoothing and genomic visualization of array dataqvalue-2.36.0 Q-value estimation for false discovery rate controlqvcalc-1.0.3 Quasi Variances for Factor Effects in Statistical Modelsr2d3-0.2.6 Interface to ‘D3’ VisualizationsrARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD ProblemsrGADEM-2.52.0 de novo motif discoveryrainbow-3.8 Bagplots, Boxplots and Rainbow Plots for Functional DatarandomForest-4.7-1.1 Breiman and Cutler’s Random Forests for Classification and
Regressionrbenchmark-1.0.0 Benchmarking routine for Rrbibutils-2.2.16 Read ‘Bibtex’ Files and Convert Between Bibliography FormatsrefGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from
‘Ensembl’ and ‘UCSC’ Genome Browsersrefund-0.1-35 Regression with Functional DataregioneR-1.36.0 Association analysis of genomic regions based on permutation testsregress-1.3-21 Gaussian Linear Models with Linear Covariance Structureregtools-1.7.0 Regression and Classification Toolsrelations-0.6-13 Data Structures and Algorithms for Relationsrelevent-1.2-1 Relational Event Modelsrepr-1.1.7 Serializable Representationsreshape-0.8.9 Flexibly Reshape Datareshape2-1.4.4 Flexibly Reshape Data: A Reboot of the Reshape Packagerestfulr-0.0.15 R Interface to RESTful Web Servicesreticulate-1.36.1 Interface to ‘Python’rex-1.2.1 Friendly Regular Expressionsrgenoud-5.9-0.10 R Version of GENetic Optimization Using Derivativesrhandsontable-0.3.8 Interface to the ‘Handsontable.js’ Libraryrhdf5-2.48.0 R Interface to HDF5rhdf5filters-1.16.0 HDF5 Compression Filtersrjags-4-15 Bayesian Graphical Models using MCMCrje-1.12.1 Miscellaneous Useful Functions for Statisticsrjson-0.2.21 JSON for Rrle-0.9.2 Common Functions for Run-Length Encoded Vectorsrms-6.8-0 Regression Modeling Strategiesrngtools-1.5.2 Utility Functions for Working with Random Number Generatorsrobustbase-0.99-2 Basic Robust Statisticsrrcov-1.7-5 Scalable Robust Estimators with High Breakdown Pointrslurm-0.6.2 Submit R Calculations to a ‘Slurm’ Clusterrsparse-0.5.1 Statistical Learning on Sparse Matricesrstan-2.32.6 R Interface to Stanrstanarm-2.32.1 Bayesian Applied Regression Modeling via Stanrstantools-2.4.0 Tools for Developing R Packages Interfacing with ‘Stan’rstatix-0.7.2 Pipe-Friendly Framework for Basic Statistical Testsrsvd-1.0.5 Randomized Singular Value Decompositionrtracklayer-1.64.0 R interface to genome annotation files and the UCSC genome browserrvcheck-0.2.1 R/Package Version Checkrzmq-0.9.13 R Bindings for ‘ZeroMQ’s2-1.1.6 Spherical Geometry Operators Using the S2 Geometry Librarysamr-3.0 SAM: Significance Analysis of Microarrayssandwich-3.1-0 Robust Covariance Matrix Estimatorsscater-1.32.0 Single-Cell Analysis Toolkit for Gene Expression Data in Rscattermore-1.2 Scatterplots with More Pointsscatterpie-0.2.2 Scatter Pie Plotscatterplot3d-0.3-44 3D Scatter Plotschoolmath-0.4.2 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 Datascs-3.2.4 Splitting Conic Solverscuttle-1.14.0 Single-Cell RNA-Seq Analysis UtilitiesseqLogo-1.70.0 Sequence logos for DNA sequence alignmentsseqminer-9.4 Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into Rsets-1.0-25 Sets, Generalized Sets, Customizable Sets and Intervalssf-1.0-16 Simple Features for Rsfsmisc-1.1-18 Utilities from ‘Seminar fuer Statistik’ ETH Zurichshadowtext-0.1.3 Shadow Text Grob and LayershinyBS-0.61.1 Twitter Bootstrap Components for ShinyshinyFiles-0.9.3 A Server-Side File System Viewer for Shinyshinycssloaders-1.0.0 Add Loading Animations to a ‘shiny’ Output While It’s
Recalculatingshinyjqui-0.4.1 ‘jQuery UI’ Interactions and Effects for Shinyshinyjs-2.1.0 Easily Improve the User Experience of Your Shiny Apps in Secondsshinystan-2.6.0 Interactive Visual and Numerical Diagnostics and Posterior
Analysis for Bayesian Modelsshinythemes-1.2.0 Themes for Shinysiggenes-1.78.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approachessitmo-2.0.2 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header
Filesslam-0.1-50 Sparse Lightweight Arrays and Matricessna-2.7-2 Tools for Social Network Analysissnow-0.4-4 Simple Network of WorkstationssnpStats-1.54.0 SnpMatrix and XSnpMatrix classes and methodssodium-1.3.1 A Modern and Easy-to-Use Crypto Librarysp-2.1-4 Classes and Methods for Spatial Datasparklyr-1.8.6 R Interface to Apache SparksparseMatrixStats-1.16.0 Summary Statistics for Rows and Columns of Sparse Matricesspatstat-3.0-8 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Testsspatstat.data-3.0-4 Datasets for ‘spatstat’ Familyspatstat.explore-3.2-7 Exploratory Data Analysis for the ‘spatstat’ Familyspatstat.geom-3.2-9 Geometrical Functionality of the ‘spatstat’ Familyspatstat.linnet-3.1-5 Linear Networks Functionality of the ‘spatstat’ Familyspatstat.model-3.2-11 Parametric Statistical Modelling and Inference for the
‘spatstat’ Familyspatstat.random-3.2-3 Random Generation Functionality for the ‘spatstat’ Familyspatstat.sparse-3.0-3 Sparse Three-Dimensional Arrays and Linear Algebra Utilitiesspatstat.utils-3.0-4 Utility Functions for ‘spatstat’sqldf-0.4-11 Manipulate R Data Frames Using SQLsquash-1.0.9 Color-Based Plots for Multivariate Visualizationsrvyr-1.2.0 ‘dplyr’-Like Syntax for Summary Statistics of Survey Datassgraph-1.15 Bayesian Graph Structure Learning using Spike-and-Slab Priorsstabledist-0.7-1 Stable Distribution Functionsstatmod-1.5.0 Statistical Modelingstatnet.common-4.9.0 Common R Scripts and Utilities Used by the Statnet Project
Softwarestringdist-0.9.12 Approximate String Matching, Fuzzy Text Search, and String
Distance Functionsstrucchange-1.5-3 Testing, Monitoring, and Dating Structural Changessurvey-4.4-2 Analysis of Complex Survey Samplessva-3.52.0 Surrogate Variable AnalysissystemPipeR-2.10.0 systemPipeR: workflow management and report generation environmenttables-0.9.25 Formula-Driven Table Generationtensor-1.5 Tensor product of arraystensorA-0.36.2.1 Advanced Tensor Arithmetic with Named Indicestergm-4.2.0 Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph ModelstergmLite-2.6.1 Fast Simulation of Simple Temporal Exponential Random Graph
Modelstext2vec-0.6.4 Modern Text Mining Framework for Rthreejs-0.3.3 Interactive 3D Scatter Plots, Networks and Globestidyposterior-1.0.1 Bayesian Analysis to Compare Models using Resampling Statisticstidytree-0.4.6 A Tidy Tool for Phylogenetic Tree Data Manipulationtiff-0.1-12 Read and Write TIFF ImagestilingArray-1.82.0 Transcript mapping with high-density oligonucleotide tiling arraystimeSeries-4032.109 Financial Time Series Objects (Rmetrics)tkWidgets-1.82.0 R based tk widgetstreeio-1.28.0 Base Classes and Functions for Phylogenetic Tree Input and Outputtriebeard-0.4.1 ‘Radix’ Trees in ‘Rcpp’truncnorm-1.0-9 Truncated Normal Distributiontrust-0.1-8 Trust Region Optimizationtweenr-2.0.3 Interpolate Data for Smooth Animationstxdbmaker-1.0.0 Tools for making TxDb objects from genomic annotationsucminf-1.2.1 General-Purpose Unconstrained Non-Linear Optimizationudunits2-0.13.2.1 Udunits-2 Bindings for Runits-0.8-5 Measurement Units for R Vectorsuniversalmotif-1.22.0 Import, Modify, and Export Motifs with Rurltools-1.7.3 Vectorised Tools for URL Handling and Parsinguwot-0.2.2 The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reductionvegan-2.6-6 Community Ecology Packagevenn-1.12 Draw Venn Diagramsvimp-2.3.3 Perform Inference on Algorithm-Agnostic Variable Importancevipor-0.4.7 Plot Categorical Data Using Quasirandom Noise and Density
Estimatesviridis-0.6.5 Colorblind-Friendly Color Maps for Rvsn-3.72.0 Variance stabilization and calibration for microarray datawavethresh-4.7.2 Wavelets Statistics and Transformswebp-1.2.0 A New Format for Lossless and Lossy Image CompressionwidgetTools-1.82.0 Creates an interactive tcltk widgetwk-0.9.1 Lightweight Well-Known Geometry ParsingxCell 1.1.0 [CRAN]
xmlparsedata-1.0.5 Parse Data of ‘R’ Code as an ‘XML’ Treexts-0.13.2 eXtensible Time Seriesyulab.utils-0.1.4 Supporting Functions for Packages Maintained by ‘YuLab-SMU’zCompositions-1.5.0-3 Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Setszlibbioc-1.50.0 An R packaged zlib-1.2.5zoo-1.8-12 S3 Infrastructure for Regular and Irregular Time Series (Z’s
Ordered Observations)