Known Issues
Package List
ADGofTest-0.3 Anderson-Darling GoF testAICcmodavg-2.3-1 Model Selection and Multimodel Inference Based on (Q)AIC(c)ALDEx2-1.22.0 Analysis Of Differential Abundance Taking Sample Variation Into AccountALL-1.32.0 A data packageASCAT 2.5.2
AUC-0.3.0 Threshold independent performance measures for probabilistic<U+000a>classifiers.AgiMicroRna-2.40.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAlgDesign-1.2.0 Algorithmic Experimental DesignAnalyzeFMRI-1.1-23 Functions for Analysis of fMRI Datasets Stored in the ANALYZE or
NIFTI FormatAnnotationDbi-1.52.0 Manipulation of SQLite-based annotations in BioconductorAnnotationFilter-1.14.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.32.0 Tools for building SQLite-based annotation data packagesAnnotationHub-2.22.0 Client to access AnnotationHub resourcesArchR 1.0.1
BB-2019.10-1 Solving and Optimizing Large-Scale Nonlinear SystemsBBmisc-1.11 Miscellaneous Helper Functions for B. BischlBCEE-1.3.0 The Bayesian Causal Effect Estimation AlgorithmBDgraph-2.63 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMCBH-1.75.0-0 Boost C++ Header FilesBIGL-1.6.2 Biochemically Intuitive Generalized Loewe ModelBMA-3.18.14 Bayesian Model AveragingBSgenome-1.58.0 Software infrastructure for efficient representation of full genomes and their SNPsBSgenome.Hsapiens.UCSC.hg19-1.4.3 Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)BatchJobs-1.8 Batch Computing with RBayesPen-1.0 Bayesian Penalized Credible RegionsBayesianTools-0.1.7 General-Purpose MCMC and SMC Samplers and Tools for Bayesian
StatisticsBhat-0.9-10 General likelihood explorationBiasedUrn-1.07 Biased Urn Model DistributionsBiobase-2.50.0 Biobase: Base functions for BioconductorBiocFileCache-1.14.0 Manage Files Across SessionsBiocGenerics-0.36.0 S4 generic functions used in BioconductorBiocManager-1.30.12 Access the Bioconductor Project Package RepositoryBiocParallel-1.24.1 Bioconductor facilities for parallel evaluationBiocStyle-2.18.1 Standard styles for vignettes and other Bioconductor documentsBiocVersion-3.12.0 Set the appropriate version of Bioconductor packagesBiostrings-2.58.0 Efficient manipulation of biological stringsBivarP-1.0 Estimating the Parameters of Some Bivariate DistributionsBolstad-0.2-41 Functions for Elementary Bayesian InferenceBolstad2-1.0-28 Bolstad functionsBoruta-7.0.0 Wrapper Algorithm for All Relevant Feature SelectionBradleyTerry2-1.1-2 Bradley-Terry ModelsBrobdingnag-1.2-6 Very Large Numbers in RCGHbase-1.50.0 CGHbase: Base functions and classes for arrayCGH data analysis.CLONETv2-2.1.0 Clonality Estimates in TumorCMA-1.48.0 Synthesis of microarray-based classificationCNEr-1.26.0 CNE Detection and VisualizationCOMPASS-1.28.0 Combinatorial Polyfunctionality Analysis of Single CellsCVST-0.2-2 Fast Cross-Validation via Sequential TestingCairo-1.5-12.2 R Graphics Device using Cairo Graphics Library for Creating
High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG,
PostScript) and Display (X11 and Win32) OutputCategory-2.56.0 Category AnalysisChIPpeakAnno-3.24.2 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome rangesChIPseeker-1.26.2 ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationComICS-1.0.4 Computational Methods for Immune Cell-Type SubsetsCompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal VariablesComplexHeatmap-2.6.2 Make Complex HeatmapsConsensusClusterPlus-1.54.0 ConsensusClusterPlusCovSel-1.2.1 Model-Free Covariate SelectionCytoML-2.2.2 A GatingML Interface for Cross Platform Cytometry Data SharingDAAG-1.24 Data Analysis and Graphics Data and FunctionsDBI-1.1.1 R Database InterfaceDECIPHER-2.18.1 Tools for curating, analyzing, and manipulating biological sequencesDEGseq-1.44.0 Identify Differentially Expressed Genes from RNA-seq dataDESeq2-1.30.1 Differential gene expression analysis based on the negative binomial distributionDEoptimR-1.0-8 Differential Evolution Optimization in Pure RDHARMa-0.4.0 Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression ModelsDNAcopy-1.64.0 DNA copy number data analysisDO.db-2.9 A set of annotation maps describing the entire Disease OntologyDOSE-3.16.0 Disease Ontology Semantic and Enrichment analysisDOT-0.1 Render and Export DOT Graphs in RDRR-0.0.4 Dimensionality Reduction via RegressionDT-0.17 A Wrapper of the JavaScript Library ‘DataTables’DTRreg-1.7 DTR Estimation and Inference via G-Estimation, Dynamic WOLS,
Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)DelayedArray-0.16.3 A unified framework for working transparently with on-disk and in-memory array-like datasetsDelayedMatrixStats-1.12.3 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ ObjectsDeriv-4.1.3 Symbolic DifferentiationDescTools-0.99.40 Tools for Descriptive StatisticsDiagrammeR-1.0.6.1 Graph/Network VisualizationDiceDesign-1.9 Designs of Computer ExperimentsDiffBind-3.0.15 Differential Binding Analysis of ChIP-Seq Peak DataDirichletMultinomial-1.32.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataDiscriMiner-0.1-29 Tools of the Trade for Discriminant AnalysisDistributionUtils-0.6-0 Distribution UtilitiesDynDoc-1.68.0 Dynamic document toolsEBImage-4.32.0 Image processing and analysis toolbox for RENMeval-0.3.1 Automated Tuning and Evaluations of Ecological Niche ModelsEasyABC-1.5 Efficient Approximate Bayesian Computation Sampling SchemesEnvStats-2.4.0 Package for Environmental Statistics, Including US EPA GuidanceEpiModel-2.0.3 Mathematical Modeling of Infectious Disease DynamicsExact-2.1 Unconditional Exact TestFDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probesFME-1.3.6.1 A Flexible Modelling Environment for Inverse Modelling,
Sensitivity, Identifiability and Monte Carlo AnalysisFNN-1.1.3 Fast Nearest Neighbor Search Algorithms and ApplicationsFactoMineR-2.4 Multivariate Exploratory Data Analysis and Data MiningFlowSOM-1.22.0 Using self-organizing maps for visualization and interpretation of cytometry dataFormula-1.2-4 Extended Model FormulasGENESIS-2.20.1 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessGEOquery-2.58.0 Get data from NCBI Gene Expression Omnibus (GEO)GGally-2.1.1 Extension to ‘ggplot2’GO.db-3.12.1 A set of annotation maps describing the entire Gene OntologyGOSemSim-2.16.1 GO-terms Semantic Similarity MeasuresGOstats-2.56.0 Tools for manipulating GO and microarraysGPfit-1.0-8 Gaussian Processes ModelingGSA-1.03.1 Gene Set AnalysisGSEABase-1.52.1 Gene set enrichment data structures and methodsGSVA-1.38.2 Gene Set Variation Analysis for microarray and RNA-seq dataGUTS-1.1.1 Fast Calculation of the Likelihood of a Stochastic Survival
ModelGWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association StudiesGWASTools-1.36.0 Tools for Genome Wide Association StudiesGenSA-1.1.7 Generalized Simulated AnnealingGeneNet-1.2.15 Modeling and Inferring Gene NetworksGenomeGraphs 1.46.0
GenomeInfoDb-1.26.7 Utilities for manipulating chromosome names, including modifying them to follow a particular naming styleGenomeInfoDbData-1.2.4 Species and taxonomy ID look up tables used by GenomeInfoDbGenomicAlignments-1.26.0 Representation and manipulation of short genomic alignmentsGenomicFeatures-1.42.3 Conveniently import and query gene modelsGenomicFiles-1.26.0 Distributed computing by file or by rangeGenomicRanges-1.42.0 Representation and manipulation of genomic intervalsGetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable InterpolationGillespieSSA-0.6.1 Gillespie’s Stochastic Simulation Algorithm (SSA)Glimma-2.0.0 Interactive HTML graphicsGlobalOptions-0.1.2 Generate Functions to Get or Set Global OptionsGmisc-2.0.1 Descriptive Statistics, Transition Plots, and MoreGreyListChIP-1.22.0 Grey Lists – Mask Artefact Regions Based on ChIP InputsGviz-1.34.1 Plotting data and annotation information along genomic coordinatesHDF5Array-1.18.1 HDF5 backend for DelayedArray objectsHMMcopy-1.32.0 Copy number prediction with correction for GC and mappability bias for HTS dataHSMMSingleCell-1.10.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)HWxtest-1.1.9 Exact Tests for Hardy-Weinberg ProportionsHaploSim-1.8.4 Functions to simulate haplotypesHiddenMarkov-1.8-11 Hidden Markov ModelsHmisc-4.5-0 Harrell MiscellaneousHomo.sapiens-1.3.1 Annotation package for the Homo.sapiens objectIDPmisc-1.1.20 ‘Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)’IHW-1.18.0 Independent Hypothesis WeightingIRanges-2.24.1 Foundation of integer range manipulation in BioconductorIRdisplay-1.0 ‘Jupyter’ Display MachineryISOcodes-2021.02.24 Selected ISO CodesIlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arraysIso-0.0-18.1 Functions to Perform Isotonic RegressionJADE-2.0-3 Blind Source Separation Methods Based on Joint Diagonalization
and Some BSS Performance CriteriaJBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J.
ButtlarKEGG.db-3.2.4 A set of annotation maps for KEGGKEGGREST-1.30.1 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)KEGGgraph-1.50.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorKEGGprofile-1.32.0 An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathwayKODAMA-1.5 Knowledge Discovery by Accuracy MaximizationKernSmooth-2.23-18 Functions for Kernel Smoothing Supporting Wand & Jones (1995)LaplacesDemon-16.1.4 Complete Environment for Bayesian InferenceLearnBayes-2.15.1 Functions for Learning Bayesian InferenceLmoments-1.3-1 L-Moments and Quantile MixturesLogicReg-1.6.2 Logic RegressionLymphoSeq-1.18.0 Analyze high-throughput sequencing of T and B cell receptorsLymphoSeqDB-0.99.2 LymphoSeq annotation databasesMAGeCKFlute-1.10.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic ScreensMALDIquant-1.19.3 Quantitative Analysis of Mass Spectrometry DataMASS-7.3-53.1 Support Functions and Datasets for Venables and Ripley’s MASSMAST-1.16.0 Model-based Analysis of Single Cell TranscriptomicsMCMCglmm-2.32 MCMC Generalised Linear Mixed ModelsMCMCpack-1.5-0 Markov Chain Monte Carlo (MCMC) PackageMIIVsem-0.5.5 Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation ModelsMPV-1.57 Data Sets from Montgomery, Peck and ViningMatchIt-4.1.0 Nonparametric Preprocessing for Parametric Causal InferenceMatching-4.9-7 Multivariate and Propensity Score Matching with Balance
OptimizationMatrix-1.3-2 Sparse and Dense Matrix Classes and MethodsMatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
OperationsMatrixGenerics-1.2.1 S4 Generic Summary Statistic Functions that Operate on Matrix-Like ObjectsMatrixModels-0.5-0 Modelling with Sparse and Dense MatricesMfuzz-2.50.0 Soft clustering of time series gene expression dataModelMetrics-1.2.2.2 Rapid Calculation of Model MetricsNADA-1.6-1.1 Nondetects and Data Analysis for Environmental DataNCmisc-1.1.6 Miscellaneous Functions for Creating Adaptive Functions and
ScriptsNISTunits-1.0.1 Fundamental Physical Constants and Unit Conversions from NISTNLP-0.2-1 Natural Language Processing InfrastructureNOISeq-2.34.0 Exploratory analysis and differential expression for RNA-seq dataOrganismDbi-1.32.0 Software to enable the smooth interfacing of different database packagesPBSddesolve-1.12.6 Solver for Delay Differential EquationsPFAM.db-3.12.0 A set of protein ID mappings for PFAMPICS-2.34.0 Probabilistic inference of ChIP-seqParamHelpers-1.14 Helpers for Parameters in Black-Box Optimization, Tuning and
Machine LearningPermAlgo-1.1 Permutational Algorithm to Simulate Survival DataPoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log
linear modelPolynomF-2.0-3 Polynomials in RPresenceAbsence-1.1.9 Presence-Absence Model Evaluation.ProtGenerics-1.22.0 S4 generic functions for Bioconductor proteomics infrastructureQUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix EstimationR.cache-0.14.0 Fast and Light-Weight Caching (Memoization) of Objects and
Results to Speed Up ComputationsR.matlab-3.6.2 Read and Write MAT Files and Call MATLAB from Within RR.methodsS3-1.8.1 S3 Methods SimplifiedR.oo-1.24.0 R Object-Oriented Programming with or without ReferencesR.rsp-0.44.0 Dynamic Generation of Scientific ReportsR.utils-2.10.1 Various Programming UtilitiesR2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’R2jags-0.6-1 Using R to Run ‘JAGS’R6-2.5.0 Encapsulated Classes with Reference SemanticsRANN-2.6.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
MetricRBGL-1.66.0 An interface to the BOOST graph libraryRCAL-2.0 Regularized Calibrated EstimationRCircos-1.2.1 Circos 2D Track PlotRColorBrewer-1.1-2 ColorBrewer PalettesRCurl-1.98-1.3 General Network (HTTP/FTP/…) Client Interface for RREDCapR-0.11.0 Interaction Between R and REDCapRGCCA-2.1.2 Regularized and Sparse Generalized Canonical Correlation
Analysis for Multiblock DataRInside-0.2.16 C++ Classes to Embed R in C++ (and C) ApplicationsRItools-0.1-17 Randomization Inference ToolsRJSONIO-1.3-1.4 Serialize R Objects to JSON, JavaScript Object NotationRLRsim-3.1-6 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
ModelsRMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix<U+000a>TheoryRNASeqPower-1.30.0 Sample size for RNAseq studiesRNeXML-2.4.5 Semantically Rich I/O for the ‘NeXML’ FormatRNifti-1.3.0 Fast R and C++ Access to NIfTI ImagesROCR-1.0-11 Visualizing the Performance of Scoring ClassifiersROI-1.0-0 R Optimization InfrastructureROI.plugin.glpk-1.0-0 ‘ROI’ Plug-in ‘GLPK’RPMM-1.25 Recursively Partitioned Mixture ModelRPostgreSQL-0.6-2 R Interface to the ‘PostgreSQL’ Database SystemRPresto-1.3.5 DBI Connector to PrestoRProtoBufLib-2.2.0 C++ headers and static libraries of Protocol buffersRSNNS-0.4-12 Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)RSQLite-2.2.5 ‘SQLite’ Interface for RRSclient-0.7-3 Client for RserveRSpectra-0.16-0 Solvers for Large-Scale Eigenvalue and SVD ProblemsRUnit-0.4.32 R Unit Test FrameworkRWeka-0.4-43 R/Weka InterfaceRWekajars-3.9.3-2 R/Weka Interface JarsRborist-0.2-3 Extensible, Parallelizable Implementation of the Random Forest
AlgorithmRcpp-1.0.6 Seamless R and C++ IntegrationRcppAnnoy-0.0.18 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
NeighborsRcppArmadillo-0.10.2.2.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra
LibraryRcppCCTZ-0.2.9 ‘Rcpp’ Bindings for the ‘CCTZ’ LibraryRcppDate-0.0.2 ‘date’ C++ Header Library for Date and Time FunctionalityRcppEigen-0.3.3.9.1 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra
LibraryRcppGSL-0.3.8 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and MatricesRcppNumerical-0.4-0 ‘Rcpp’ Integration for Numerical Computing LibrariesRcppParallel-5.0.3 Parallel Programming Tools for ‘Rcpp’RcppProgress-0.4.2 An Interruptible Progress Bar with OpenMP Support for C++ in R
PackagesRcppRoll-0.3.0 Efficient Rolling / Windowed OperationsRdpack-2.1.1 Update and Manipulate Rd Documentation ObjectsRdsdp-1.0.5 R Interface to DSDP Semidefinite Programming LibraryRefFreeEWAS-2.2 EWAS using Reference-Free DNA Methylation Mixture DeconvolutionReportingTools-2.30.2 Tools for making reports in various formatsRglpk-0.6-4 R/GNU Linear Programming Kit InterfaceRgraphviz-2.34.0 Provides plotting capabilities for R graph objectsRhdf5lib-1.12.1 hdf5 library as an R packageRhpc-0.19-276 Permits *apply() Style Dispatch for ‘HPC’Rhtslib-1.22.0 HTSlib high-throughput sequencing library as an R packageRingo-1.54.0 R Investigation of ChIP-chip OligoarraysRlabkey-2.6.0 Data Exchange Between R and ‘LabKey’ ServerRmpi-0.6-9.1 Interface (Wrapper) to MPI (Message-Passing Interface)Rook-1.1-1 Rook - a web server interface for RRsamtools-2.6.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importRserve-1.7-3.1 Binary R serverRssa-1.0.3 A Collection of Methods for Singular Spectrum AnalysisRsubread-2.4.3 Mapping, quantification and variant analysis of sequencing dataRtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
ImplementationRttf2pt1-1.3.8 ‘ttf2pt1’ ProgramS4Vectors-0.28.1 Foundation of vector-like and list-like containers in BioconductorSDMTools-1.1-221.2 Species Distribution Modelling Tools: Tools for processing data
associated with species distribution modelling exercisesSKAT-2.0.1 SNP-Set (Sequence) Kernel Association TestSNPRelate-1.24.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)SNPassoc-2.0-2 SNPs-Based Whole Genome Association StudiesSOAR-0.99-11 Memory management in R by delayed assignmentsSPAtest-3.1.2 Score Test and Meta-Analysis Based on Saddlepoint ApproximationSPIA-2.42.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsSQUAREM-2021.1 Squared Extrapolation Methods for Accelerating EM-Like Monotone
AlgorithmsSemiPar-1.0-4.2 Semiparametic RegressionSeqArray-1.30.0 Data management of large-scale whole-genome sequence variant callsSeqVarTools-1.28.1 Tools for variant dataShortRead-1.48.0 FASTQ input and manipulationSignifReg-3.0 Consistent Significance Controlled Variable Selection in
Generalized Linear RegressionSimSeq-1.4.0 Nonparametric Simulation of RNA-Seq DataSingleCellExperiment-1.12.0 S4 Classes for Single Cell DataSnowballC-0.7.0 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 LibrarySparseM-1.81 Sparse Linear AlgebraStanHeaders-2.21.0-7 C++ Header Files for StanSummarizedExperiment-1.20.0 SummarizedExperiment containerSuperLearner-2.0-26 Super Learner PredictionSuppDists-1.1-9.5 Supplementary DistributionsTFBSTools-1.28.0 Software Package for Transcription Factor Binding Site (TFBS) AnalysisTFMPvalue-0.0.8 Efficient and Accurate P-Value Computation for Position Weight
MatricesTFisher-0.2.0 Optimal Thresholding Fisher’s P-Value Combination MethodTH.data-1.0-10 TH’s Data ArchiveTMB-1.7.19 Template Model Builder: A General Random Effect Tool Inspired by
‘ADMB’TTR-0.24.2 Technical Trading RulesTeachingDemos-2.12 Demonstrations for Teaching and LearningTitanCNA-1.28.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumoursTraMineR-2.2-1 Trajectory Miner: a Toolbox for Exploring and Rendering
SequencesTxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)UpSetR-1.4.0 A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting SetsV8-3.4.0 Embedded JavaScript and WebAssembly Engine for RVGAM-1.1-5 Vector Generalized Linear and Additive ModelsVIM-6.1.0 Visualization and Imputation of Missing ValuesVSURF-1.1.0 Variable Selection Using Random ForestsVariantAnnotation-1.36.0 Annotation of Genetic VariantsVennDiagram-1.6.20 Generate High-Resolution Venn and Euler PlotsWeightSVM-1.7-5 Subject Weighted Support Vector MachinesWikidataR-1.4.0 Read-Write API Client Library for ‘Wikidata’WikipediR-1.5.0 A MediaWiki API WrapperWrench-1.8.0 Wrench normalization for sparse count dataWriteXLS-6.2.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) FilesXML-3.99-0.6 Tools for Parsing and Generating XML Within R and S-PlusXVector-0.30.0 Foundation of external vector representation and manipulation in Bioconductorabc-2.1 Tools for Approximate Bayesian Computation (ABC)abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)abe-3.0.1 Augmented Backward Eliminationabind-1.4-5 Combine Multidimensional Arraysacepack-1.4.1 ACE and AVAS for Selecting Multiple Regression Transformationsadabag-4.2 Applies Multiclass AdaBoost.M1, SAMME and Baggingade4-1.7-16 Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciencesadmisc-0.12 Adrian Dusa’s Miscellaneousaffy-1.68.0 Methods for Affymetrix Oligonucleotide Arraysaffycoretools-1.62.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChipsaffyio-1.60.0 Tools for parsing Affymetrix data filesaggregation-1.0.1 p-Value Aggregation Methodsakima-0.6-2.1 Interpolation of Irregularly and Regularly Spaced Dataalr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Editionamap-0.8-18 Another Multidimensional Analysis Packageanimation-2.6 A Gallery of Animations in Statistics and Utilities to Create
Animationsannaffy-1.62.0 Annotation tools for Affymetrix biological metadataannotate-1.68.0 Annotation for microarraysaod-1.3.1 Analysis of Overdispersed Dataape-5.4-1 Analyses of Phylogenetics and Evolutionapeglm-1.12.0 Approximate posterior estimation for GLM coefficientsaplot-0.0.6 Decorate a ‘ggplot’ with Associated Informationargparse-2.0.3 Command Line Optional and Positional Argument Parserargparser-0.7.1 Command-Line Argument Parserarm-1.11-2 Data Analysis Using Regression and Multilevel/Hierarchical
Modelsarsenal-3.6.2 An Arsenal of ‘R’ Functions for Large-Scale Statistical
Summariesarules-1.6-7 Mining Association Rules and Frequent Itemsetsash-1.0-15 David Scott’s ASH Routinesashr-2.2-47 Methods for Adaptive Shrinkage, using Empirical Bayesaskpass-1.1 Safe Password Entry for R, Git, and SSHasnipe-1.1.15 Animal Social Network Inference and Permutations for Ecologistsassertive-0.3-6 Readable Check Functions to Ensure Code Integrityassertive.base-0.0-9 A Lightweight Core of the ‘assertive’ Packageassertive.code-0.0-3 Assertions to Check Properties of Codeassertive.data-0.0-3 Assertions to Check Properties of Dataassertive.data.uk-0.0-2 Assertions to Check Properties of Stringsassertive.data.us-0.0-2 Assertions to Check Properties of Stringsassertive.datetimes-0.0-3 Assertions to Check Properties of Dates and Timesassertive.files-0.0-2 Assertions to Check Properties of Filesassertive.matrices-0.0-2 Assertions to Check Properties of Matricesassertive.models-0.0-2 Assertions to Check Properties of Modelsassertive.numbers-0.0-2 Assertions to Check Properties of Numbersassertive.properties-0.0-4 Assertions to Check Properties of Variablesassertive.reflection-0.0-5 Assertions for Checking the State of Rassertive.sets-0.0-3 Assertions to Check Properties of Setsassertive.strings-0.0-3 Assertions to Check Properties of Stringsassertive.types-0.0-3 Assertions to Check Types of Variablesassertthat-0.2.1 Easy Pre and Post Assertionsaudio-0.1-7 Audio Interface for Raws-2.5-1 Adaptive Weights Smoothingaws.ec2metadata-0.2.0 Get EC2 Instance Metadataaws.s3-0.3.21 ‘AWS S3’ Client Packageaws.signature-0.6.0 Amazon Web Services Request SignaturesawsMethods-1.1-1 Class and Methods Definitions for Packages ‘aws’, ‘adimpro’,
‘fmri’, ‘dwi’backports-1.2.1 Reimplementations of Functions Introduced Since R-3.0.0bacr-1.0.1 Bayesian Adjustment for Confoundingbamsignals-1.22.0 Extract read count signals from bam filesbartMachine-1.2.6 Bayesian Additive Regression TreesbartMachineJARs-1.1 bartMachine JARsbase built in
base64-2.0 Base64 Encoder and Decoderbase64enc-0.1-3 Tools for base64 encodingbase64url-1.4 Fast and URL-Safe Base64 Encoder and Decoderbatchmeans-1.0-4 Consistent Batch Means Estimation of Monte Carlo Standard Errorsbatchtools-0.9.15 Tools for Computation on Batch SystemsbaySeq-2.24.0 Empirical Bayesian analysis of patterns of differential expression in count databayesm-3.1-4 Bayesian Inference for Marketing/Micro-Econometricsbayesplot-1.8.0 Plotting for Bayesian Modelsbbmle-1.0.23.1 Tools for General Maximum Likelihood Estimationbdsmatrix-1.3-4 Routines for Block Diagonal Symmetric Matricesbeanplot-1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin<U+000a>Plot)beeswarm-0.3.1 The Bee Swarm Plot, an Alternative to Stripchartbenchmark-0.3-6 Benchmark Experiments Toolboxbetareg-3.1-4 Beta Regressionbezier-1.1.2 Toolkit for Bezier Curves and Splinesbibtex-0.4.2.3 Bibtex Parserbiglm-0.9-2.1 Bounded Memory Linear and Generalized Linear Modelsbigmemory-4.5.36 Manage Massive Matrices with Shared Memory and Memory-Mapped
Filesbigmemory.sri-0.1.3 A shared resource interface for Bigmemory Project packagesbindr-0.1.1 Parametrized Active Bindingsbindrcpp-0.2.2 An ‘Rcpp’ Interface to Active Bindingsbio3d-2.4-1 Biological Structure Analysisbiom-0.3.12 An interface package (beta) for the BIOM file format.biomaRt-2.46.3 Interface to BioMart databases (i.e. Ensembl)biomformat-1.18.0 An interface package for the BIOM file formatbiovizBase-1.38.0 Basic graphic utilities for visualization of genomic data.bit-4.0.4 Classes and Methods for Fast Memory-Efficient Boolean Selectionsbit64-4.0.5 A S3 Class for Vectors of 64bit Integersbitops-1.0-6 Bitwise Operationsblavaan-0.3-15 Bayesian Latent Variable Analysisblob-1.2.1 A Simple S3 Class for Representing Vectors of Binary Data
(‘BLOBS’)bmp-0.3 Read Windows Bitmap (BMP) Imagesbnlearn-4.6.1 Bayesian Network Structure Learning, Parameter Learning and
Inferencebold-1.1.0 Interface to Bold Systems APIbookdown-0.21 Authoring Books and Technical Documents with R Markdownboot-1.3-27 Bootstrap Functions (Originally by Angelo Canty for S)bootstrap-2019.6 Functions for the Book “An Introduction to the Bootstrap”breakaway-3.0 Species Richness Estimation and Modelingbrew-1.0-6 Templating Framework for Report Generationbrglm-0.7.1 Bias Reduction in Binomial-Response Generalized Linear Modelsbridgedist-0.1.0 An Implementation of the Bridge Distribution with Logit-Link as
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Related Functionalityloo-2.4.1 Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
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Estimatesviridis-0.5.1 Colorblind-Friendly Color Maps for RviridisLite-0.3.0 Colorblind-Friendly Color Maps (Lite Version)visNetwork-2.0.9 Network Visualization using ‘vis.js’ Libraryvsn-3.58.0 Variance stabilization and calibration for microarray datawaldo-0.2.5 Find Differences Between R Objectswarp-0.2.0 Group Dateswaveslim-1.8.2 Basic Wavelet Routines for One-, Two-, and Three-Dimensional
Signal Processingwavethresh-4.6.8 Wavelets Statistics and Transformswebp-1.0 A New Format for Lossless and Lossy Image Compressionwebshot-0.5.2 Take Screenshots of Web Pageswhisker-0.4 for R, Logicless TemplatingwidgetTools-1.68.0 Creates an interactive tcltk widgetwikitaxa-0.4.0 Taxonomic Information from ‘Wikipedia’withr-2.4.1 Run Code ‘With’ Temporarily Modified Global Statewordcloud-2.6 Word Cloudsworkflows-0.2.2 Modeling Workflowsworkflowsets-0.0.1 Create a Collection of ‘tidymodels’ Workflowsworrms-0.4.2 World Register of Marine Species (WoRMS) ClientxCell 1.1.0
xfun-0.22 Supporting Functions for Packages Maintained by ‘Yihui Xie’xgboost-1.3.2.1 Extreme Gradient Boostingxlsx-0.6.5 Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Filesxlsxjars-0.6.1 Package required POI jars for the xlsx packagexml2-1.3.2 Parse XMLxmlparsedata-1.0.5 Parse Data of ‘R’ Code as an ‘XML’ Treexopen-1.0.0 Open System Files, ‘URLs’, Anythingxtable-1.8-4 Export Tables to LaTeX or HTMLxts-0.12.1 eXtensible Time SeriesyaImpute-1.0-32 Nearest Neighbor Observation Imputation and Evaluation Toolsyaml-2.2.1 Methods to Convert R Data to YAML and Backyardstick-0.0.8 Tidy Characterizations of Model PerformancezCompositions-1.3.4 Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Setszeallot-0.1.0 Multiple, Unpacking, and Destructuring Assignmentzip-2.1.1 Cross-Platform ‘zip’ Compressionzlibbioc-1.36.0 An R packaged zlib-1.2.5zoo-1.8-9 S3 Infrastructure for Regular and Irregular Time Series (Z’s
Ordered Observations)
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