Known Issues
Package List
ADGofTest-0.3 Anderson-Darling GoF testAICcmodavg-2.3-1 Model Selection and Multimodel Inference Based on (Q)AIC(c)ALDEx2-1.24.0 Analysis Of Differential Abundance Taking Sample Variation Into AccountALL-1.34.0 A data packageASCAT 2.5.2
AUC-0.3.0 Threshold independent performance measures for probabilistic<U+000a>classifiers.AgiMicroRna-2.42.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAlgDesign-1.2.0 Algorithmic Experimental DesignAnalyzeFMRI-1.1-23 Functions for Analysis of fMRI Datasets Stored in the ANALYZE or
NIFTI FormatAnnotationDbi-1.54.1 Manipulation of SQLite-based annotations in BioconductorAnnotationFilter-1.16.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.34.0 Tools for building SQLite-based annotation data packagesAnnotationHub-3.0.1 Client to access AnnotationHub resourcesArchR 1.0.1
BB-2019.10-1 Solving and Optimizing Large-Scale Nonlinear SystemsBBmisc-1.11 Miscellaneous Helper Functions for B. BischlBCEE-1.3.0 The Bayesian Causal Effect Estimation AlgorithmBDgraph-2.64 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMCBH-1.75.0-0 Boost C++ Header FilesBIGL-1.6.4 Biochemically Intuitive Generalized Loewe ModelBMA-3.18.15 Bayesian Model AveragingBSgenome-1.60.0 Software infrastructure for efficient representation of full genomes and their SNPsBSgenome.Hsapiens.UCSC.hg19-1.4.3 Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)BatchJobs-1.8 Batch Computing with RBayesPen-1.0 Bayesian Penalized Credible RegionsBayesianTools-0.1.7 General-Purpose MCMC and SMC Samplers and Tools for Bayesian
StatisticsBhat-0.9-10 General likelihood explorationBiasedUrn-1.07 Biased Urn Model DistributionsBiobase-2.52.0 Biobase: Base functions for BioconductorBiocFileCache-2.0.0 Manage Files Across SessionsBiocGenerics-0.38.0 S4 generic functions used in BioconductorBiocIO-1.2.0 Standard Input and Output for Bioconductor PackagesBiocManager-1.30.16 Access the Bioconductor Project Package RepositoryBiocNeighbors-1.10.0 Nearest Neighbor Detection for Bioconductor PackagesBiocParallel-1.26.2 Bioconductor facilities for parallel evaluationBiocSingular-1.8.1 Singular Value Decomposition for Bioconductor PackagesBiocStyle-2.20.2 Standard styles for vignettes and other Bioconductor documentsBiocVersion-3.13.1 Set the appropriate version of Bioconductor packagesBiostrings-2.60.2 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 RCATALYST-1.16.2 Cytometry dATa anALYSis ToolsCBPS-0.22 Covariate Balancing Propensity ScoreCGHbase-1.52.0 CGHbase: Base functions and classes for arrayCGH data analysis.CLONETv2-2.1.0 Clonality Estimates in TumorCMA-1.50.0 Synthesis of microarray-based classificationCNEr-1.28.0 CNE Detection and VisualizationCOMPASS-1.30.0 Combinatorial Polyfunctionality Analysis of Single CellsCVST-0.2-2 Fast Cross-Validation via Sequential TestingCairo-1.5-12.2 R Graphics Device using Cairo Graphics Library for Creating
High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG,
PostScript) and Display (X11 and Win32) OutputCategory-2.58.0 Category AnalysisChIPpeakAnno-3.26.4 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome rangesChIPseeker-1.28.3 ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationComICS-1.0.4 Computational Methods for Immune Cell-Type SubsetsCompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal VariablesComplexHeatmap-2.8.0 Make Complex HeatmapsConsensusClusterPlus-1.56.0 ConsensusClusterPlusCovSel-1.2.1 Model-Free Covariate SelectionCytoML-2.4.0 A GatingML Interface for Cross Platform Cytometry Data SharingDAAG-1.24 Data Analysis and Graphics Data and FunctionsDBI-1.1.1 R Database InterfaceDECIPHER-2.20.0 Tools for curating, analyzing, and manipulating biological sequencesDEGseq-1.46.0 Identify Differentially Expressed Genes from RNA-seq dataDESeq2-1.32.0 Differential gene expression analysis based on the negative binomial distributionDEoptim-2.2-6 Global Optimization by Differential EvolutionDEoptimR-1.0-9 Differential Evolution Optimization in Pure RDHARMa-0.4.3 Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression ModelsDMCfun-1.3.0 Diffusion Model of Conflict (DMC) in Reaction Time TasksDNAcopy-1.66.0 DNA copy number data analysisDO.db-2.9 A set of annotation maps describing the entire Disease OntologyDOSE-3.18.2 Disease Ontology Semantic and Enrichment analysisDOT-0.1 Render and Export DOT Graphs in RDRR-0.0.4 Dimensionality Reduction via RegressionDT-0.19 A Wrapper of the JavaScript Library ‘DataTables’DTRreg-1.7 DTR Estimation and Inference via G-Estimation, Dynamic WOLS,
Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)DelayedArray-0.18.0 A unified framework for working transparently with on-disk and in-memory array-like datasetsDelayedMatrixStats-1.14.3 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ ObjectsDeriv-4.1.3 Symbolic DifferentiationDescTools-0.99.42 Tools for Descriptive StatisticsDiagrammeR-1.0.6.1 Graph/Network VisualizationDiceDesign-1.9 Designs of Computer ExperimentsDiceKriging-1.6.0 Kriging Methods for Computer ExperimentsDiffBind-3.2.6 Differential Binding Analysis of ChIP-Seq Peak DataDirichletMultinomial-1.34.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataDiscriMiner-0.1-29 Tools of the Trade for Discriminant AnalysisDistributionUtils-0.6-0 Distribution UtilitiesDynDoc-1.70.0 Dynamic document toolsEBImage-4.34.0 Image processing and analysis toolbox for RENMeval-2.0.1 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-2.1.0 Mathematical Modeling of Infectious Disease DynamicsExact-3.0 Unconditional Exact TestFDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probesFME-1.3.6.1 A Flexible Modelling Environment for Inverse Modelling,
Sensitivity, Identifiability and Monte Carlo AnalysisFNN-1.1.3 Fast Nearest Neighbor Search Algorithms and ApplicationsFactoMineR-2.4 Multivariate Exploratory Data Analysis and Data MiningFlowSOM-2.0.0 Using self-organizing maps for visualization and interpretation of cytometry dataFormula-1.2-4 Extended Model FormulasGENESIS-2.22.2 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessGEOquery-2.60.0 Get data from NCBI Gene Expression Omnibus (GEO)GGally-2.1.2 Extension to ‘ggplot2’GO.db-3.13.0 A set of annotation maps describing the entire Gene OntologyGOSemSim-2.18.1 GO-terms Semantic Similarity MeasuresGOstats-2.58.0 Tools for manipulating GO and microarraysGPfit-1.0-8 Gaussian Processes ModelingGSA-1.03.1 Gene Set AnalysisGSEABase-1.54.0 Gene set enrichment data structures and methodsGSVA-1.40.1 Gene Set Variation Analysis for microarray and RNA-seq dataGUTS-1.1.1 Fast Calculation of the Likelihood of a Stochastic Survival
ModelGWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association StudiesGWASTools-1.38.0 Tools for Genome Wide Association StudiesGenSA-1.1.7 Generalized Simulated AnnealingGeneNet-1.2.15 Modeling and Inferring Gene NetworksGenomeGraphs 1.46.0
GenomeInfoDb-1.28.4 Utilities for manipulating chromosome names, including modifying them to follow a particular naming styleGenomeInfoDbData-1.2.6 Species and taxonomy ID look up tables used by GenomeInfoDbGenomicAlignments-1.28.0 Representation and manipulation of short genomic alignmentsGenomicFeatures-1.44.2 Conveniently import and query gene modelsGenomicFiles-1.28.0 Distributed computing by file or by rangeGenomicRanges-1.44.0 Representation and manipulation of genomic intervalsGetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable InterpolationGillespieSSA-0.6.1 Gillespie’s Stochastic Simulation Algorithm (SSA)Glimma-2.2.0 Interactive HTML graphicsGlobalOptions-0.1.2 Generate Functions to Get or Set Global OptionsGmisc-2.1.0 Descriptive Statistics, Transition Plots, and MoreGreyListChIP-1.24.0 Grey Lists – Mask Artefact Regions Based on ChIP InputsGviz-1.36.2 Plotting data and annotation information along genomic coordinatesGxEScanR-2.0.2 Run GWAS/GWEIS Scans Using Binary Dosage FilesHDF5Array-1.20.0 HDF5 backend for DelayedArray objectsHMMcopy-1.34.0 Copy number prediction with correction for GC and mappability bias for HTS dataHSMMSingleCell-1.12.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)HWxtest-1.1.9 Exact Tests for Hardy-Weinberg ProportionsHaploSim-1.8.4 Functions to simulate haplotypesHiddenMarkov-1.8-13 Hidden Markov ModelsHmisc-4.5-0 Harrell MiscellaneousHomo.sapiens-1.3.1 Annotation package for the Homo.sapiens objectIDPmisc-1.1.20 ‘Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)’IHW-1.20.0 Independent Hypothesis WeightingIRanges-2.26.0 Foundation of integer range manipulation in BioconductorIRdisplay-1.0 ‘Jupyter’ Display MachineryISOcodes-2021.02.24 Selected ISO CodesIlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arraysInteractionSet-1.20.0 Base Classes for Storing Genomic Interaction DataIso-0.0-18.1 Functions to Perform Isotonic RegressionJADE-2.0-3 Blind Source Separation Methods Based on Joint Diagonalization
and Some BSS Performance CriteriaJBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J.
ButtlarKEGG.db 3.2.4
KEGGREST-1.32.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)KEGGgraph-1.52.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorKEGGprofile-1.32.0 An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathwayKODAMA-1.6 Knowledge Discovery by Accuracy MaximizationKernSmooth-2.23-20 Functions for Kernel Smoothing Supporting Wand & Jones (1995)LaplacesDemon-16.1.6 Complete Environment for Bayesian InferenceLearnBayes-2.15.1 Functions for Learning Bayesian InferenceLmoments-1.3-1 L-Moments and Quantile MixturesLogicReg-1.6.4 Logic RegressionLymphoSeq-1.20.0 Analyze high-throughput sequencing of T and B cell receptorsLymphoSeqDB-0.99.2 LymphoSeq annotation databasesMAGeCKFlute-1.12.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic ScreensMALDIquant-1.20 Quantitative Analysis of Mass Spectrometry DataMASS-7.3-54 Support Functions and Datasets for Venables and Ripley’s MASSMAST-1.18.0 Model-based Analysis of Single Cell TranscriptomicsMCMCglmm-2.32 MCMC Generalised Linear Mixed ModelsMCMCpack-1.5-0 Markov Chain Monte Carlo (MCMC) PackageMIIVsem-0.5.8 Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation ModelsMPV-1.57 Data Sets from Montgomery, Peck and ViningMatchIt-4.2.0 Nonparametric Preprocessing for Parametric Causal InferenceMatching-4.9-9 Multivariate and Propensity Score Matching with Balance
OptimizationMatrix-1.3-4 Sparse and Dense Matrix Classes and MethodsMatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
OperationsMatrixGenerics-1.4.3 S4 Generic Summary Statistic Functions that Operate on Matrix-Like ObjectsMatrixModels-0.5-0 Modelling with Sparse and Dense MatricesMfuzz-2.52.0 Soft clustering of time series gene expression dataModelMetrics-1.2.2.2 Rapid Calculation of Model MetricsNADA-1.6-1.1 Nondetects and Data Analysis for Environmental DataNCmisc-1.1.6 Miscellaneous Functions for Creating Adaptive Functions and
ScriptsNISTunits-1.0.1 Fundamental Physical Constants and Unit Conversions from NISTNLP-0.2-1 Natural Language Processing InfrastructureNOISeq-2.36.0 Exploratory analysis and differential expression for RNA-seq dataOceanView-1.0.6 Visualisation of Oceanographic Data and Model OutputOrganismDbi-1.34.0 Software to enable the smooth interfacing of different database packagesPBSddesolve-1.12.6 Solver for Delay Differential EquationsPCAmatchR-0.3.0 Match Cases to Controls Based on Genotype Principal ComponentsPFAM.db-3.13.0 A set of protein ID mappings for PFAMPICS-2.36.0 Probabilistic inference of ChIP-seqParamHelpers-1.14 Helpers for Parameters in Black-Box Optimization, Tuning and
Machine LearningPermAlgo-1.1 Permutational Algorithm to Simulate Survival DataPoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log
linear modelPolynomF-2.0-3 Polynomials in RPresenceAbsence-1.1.9 Presence-Absence Model Evaluation.ProtGenerics-1.24.0 Generic infrastructure for Bioconductor mass spectrometry packagesQUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix EstimationR.cache-0.15.0 Fast and Light-Weight Caching (Memoization) of Objects and
Results to Speed Up ComputationsR.matlab-3.6.2 Read and Write MAT Files and Call MATLAB from Within RR.methodsS3-1.8.1 S3 Methods SimplifiedR.oo-1.24.0 R Object-Oriented Programming with or without ReferencesR.rsp-0.44.0 Dynamic Generation of Scientific ReportsR.utils-2.10.1 Various Programming UtilitiesR2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’R2jags-0.7-1 Using R to Run ‘JAGS’R6-2.5.1 Encapsulated Classes with Reference SemanticsRANN-2.6.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
MetricRBGL-1.68.0 An interface to the BOOST graph libraryRCAL-2.0 Regularized Calibrated EstimationRCircos-1.2.1 Circos 2D Track PlotRColorBrewer-1.1-2 ColorBrewer PalettesRCurl-1.98-1.4 General Network (HTTP/FTP/…) Client Interface for RREDCapR-1.0.0 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-1.3-1.5 Serialize R Objects to JSON, JavaScript Object NotationRLRsim-3.1-6 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
ModelsRMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix<U+000a>TheoryRNASeqPower-1.32.0 Sample size for RNAseq studiesRNeXML-2.4.5 Semantically Rich I/O for the ‘NeXML’ FormatRNifti-1.3.1 Fast R and C++ Access to NIfTI ImagesROCR-1.0-11 Visualizing the Performance of Scoring ClassifiersROI-1.0-0 R Optimization InfrastructureROI.plugin.glpk-1.0-0 ‘ROI’ Plug-in ‘GLPK’RPMM-1.25 Recursively Partitioned Mixture ModelRPostgreSQL-0.7 R Interface to the ‘PostgreSQL’ Database SystemRPresto-1.3.7 DBI Connector to PrestoRProtoBuf-0.4.17 R Interface to the ‘Protocol Buffers’ ‘API’ (Version 2 or 3)RProtoBufLib-2.4.0 C++ headers and static libraries of Protocol buffersRSNNS-0.4-14 Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)RSQLite-2.2.8 ‘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
AlgorithmRcgmin-2013-2.21 Conjugate Gradient Minimization of Nonlinear FunctionsRcpp-1.0.7 Seamless R and C++ IntegrationRcppAnnoy-0.0.19 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
NeighborsRcppArmadillo-0.10.6.0.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra
LibraryRcppCCTZ-0.2.9 ‘Rcpp’ Bindings for the ‘CCTZ’ LibraryRcppDate-0.0.3 ‘date’ C++ Header Library for Date and Time FunctionalityRcppEigen-0.3.3.9.1 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra
LibraryRcppGSL-0.3.9 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and MatricesRcppHNSW-0.3.0 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest
NeighborsRcppNumerical-0.4-0 ‘Rcpp’ Integration for Numerical Computing LibrariesRcppParallel-5.1.4 Parallel Programming Tools for ‘Rcpp’RcppProgress-0.4.2 An Interruptible Progress Bar with OpenMP Support for C++ in R
PackagesRcppRoll-0.3.0 Efficient Rolling / Windowed OperationsRcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG
ImplementationsRdpack-2.1.2 Update and Manipulate Rd Documentation ObjectsRdsdp-1.0.5 R Interface to DSDP Semidefinite Programming LibraryRefFreeEWAS-2.2 EWAS using Reference-Free DNA Methylation Mixture DeconvolutionReportingTools-2.32.1 Tools for making reports in various formatsRfast-2.0.3 A Collection of Efficient and Extremely Fast R FunctionsRglpk-0.6-4 R/GNU Linear Programming Kit InterfaceRgraphviz-2.36.0 Provides plotting capabilities for R graph objectsRhdf5lib-1.14.2 hdf5 library as an R packageRhpc-0.21-247 Permits *apply() Style Dispatch for ‘HPC’Rhtslib-1.24.0 HTSlib high-throughput sequencing library as an R packageRingo-1.56.0 R Investigation of ChIP-chip OligoarraysRlabkey-2.8.1 Data Exchange Between R and ‘LabKey’ ServerRmpi-0.6-9.1 Interface (Wrapper) to MPI (Message-Passing Interface)Rook-1.1-1 Rook - a web server interface for RRsamtools-2.8.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importRserve-1.7-3.1 Binary R serverRsolnp-1.16 General Non-Linear OptimizationRssa-1.0.3 A Collection of Methods for Singular Spectrum AnalysisRsubread-2.6.4 Mapping, quantification and variant analysis of sequencing dataRtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
ImplementationRttf2pt1-1.3.9 ‘ttf2pt1’ ProgramRvmmin-2018-4.17.1 Variable Metric Nonlinear Function MinimizationS4Vectors-0.30.0 Foundation of vector-like and list-like containers in BioconductorSBdecomp-1.1 Estimation of the Proportion of SB Explained by ConfoundersSDMTools-1.1-221.2 Species Distribution Modelling Tools: Tools for processing data
associated with species distribution modelling exercisesSKAT-2.0.1 SNP-Set (Sequence) Kernel Association TestSNPRelate-1.26.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)SNPassoc-2.0-2 SNPs-Based Whole Genome Association StudiesSOAR-0.99-11 Memory management in R by delayed assignmentsSPAtest-3.1.2 Score Test and Meta-Analysis Based on Saddlepoint ApproximationSPIA-2.44.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsSQUAREM-2021.1 Squared Extrapolation Methods for Accelerating EM-Like Monotone
AlgorithmsScaledMatrix-1.0.0 Creating a DelayedMatrix of Scaled and Centered ValuesSemiPar-1.0-4.2 Semiparametic RegressionSeqArray-1.32.0 Data management of large-scale whole-genome sequence variant callsSeqVarTools-1.30.0 Tools for variant dataShortRead-1.50.0 FASTQ input and manipulationSignifReg-4.1 Consistent Significance Controlled Variable Selection in
Generalized Linear RegressionSimSeq-1.4.0 Nonparametric Simulation of RNA-Seq DataSingleCellExperiment-1.14.1 S4 Classes for Single Cell DataSnowballC-0.7.0 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 LibrarySparseM-1.81 Sparse Linear AlgebraStanHeaders-2.21.0-7 C++ Header Files for StanSummarizedExperiment-1.22.0 SummarizedExperiment containerSuperLearner-2.0-28 Super Learner PredictionSuppDists-1.1-9.5 Supplementary DistributionsTFBSTools-1.30.0 Software Package for Transcription Factor Binding Site (TFBS) AnalysisTFMPvalue-0.0.8 Efficient and Accurate P-Value Computation for Position Weight
MatricesTFisher-0.2.0 Optimal Thresholding Fisher’s P-Value Combination MethodTH.data-1.0-10 TH’s Data ArchiveTMB-1.7.21 Template Model Builder: A General Random Effect Tool Inspired by
‘ADMB’TTR-0.24.2 Technical Trading RulesTeachingDemos-2.12 Demonstrations for Teaching and LearningTitanCNA-1.30.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumoursTraMineR-2.2-2 Trajectory Miner: a Toolbox for Exploring and Rendering
SequencesTxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)UpSetR-1.4.0 A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting SetsV8-3.4.2 Embedded JavaScript and WebAssembly Engine for RVGAM-1.1-5 Vector Generalized Linear and Additive ModelsVIM-6.1.1 Visualization and Imputation of Missing ValuesVSURF-1.1.0 Variable Selection Using Random ForestsVariantAnnotation-1.38.0 Annotation of Genetic VariantsVennDiagram-1.6.20 Generate High-Resolution Venn and Euler PlotsWeightSVM-1.7-5 Subject Weighted Support Vector MachinesWikidataQueryServiceR-1.0.0 API Client Library for ‘Wikidata Query Service’WikidataR-2.3.1 Read-Write API Client Library for ‘Wikidata’WikipediR-1.5.0 A MediaWiki API WrapperWrench-1.10.0 Wrench normalization for sparse count dataWriteXLS-6.3.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) FilesXML-3.99-0.7 Tools for Parsing and Generating XML Within R and S-PlusXVector-0.32.0 Foundation of external vector representation and manipulation in Bioconductorabc-2.1 Tools for Approximate Bayesian Computation (ABC)abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)abe-3.0.1 Augmented Backward Eliminationabind-1.4-5 Combine Multidimensional Arraysacepack-1.4.1 ACE and AVAS for Selecting Multiple Regression Transformationsadabag-4.2 Applies Multiclass AdaBoost.M1, SAMME and Baggingade4-1.7-17 Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciencesadmisc-0.18 Adrian Dusa’s Miscellaneousaffxparser-1.64.1 Affymetrix File Parsing SDKaffy-1.70.0 Methods for Affymetrix Oligonucleotide Arraysaffycoretools-1.64.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChipsaffyio-1.62.0 Tools for parsing Affymetrix data filesaggregation-1.0.1 p-Value Aggregation Methodsakima-0.6-2.2 Interpolation of Irregularly and Regularly Spaced Dataalabama-2015.3-1 Constrained Nonlinear Optimizationalr3-2.0.8 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-1.64.2 Annotation tools for Affymetrix biological metadataannotate-1.70.0 Annotation for microarraysaod-1.3.1 Analysis of Overdispersed Dataape-5.5 Analyses of Phylogenetics and Evolutionapeglm-1.14.0 Approximate posterior estimation for GLM coefficientsaplot-0.1.0 Decorate a ‘ggplot’ with Associated Informationargparse-2.0.4 Command Line Optional and Positional Argument Parserargparser-0.7.1 Command-Line Argument Parserarm-1.11-2 Data Analysis Using Regression and Multilevel/Hierarchical
Modelsarsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical
Summariesarules-1.6-8 Mining Association Rules and Frequent Itemsetsash-1.0-15 David Scott’s ASH Routinesashr-2.2-47 Methods for Adaptive Shrinkage, using Empirical Bayesaskpass-1.1 Safe Password Entry for R, Git, and SSHasnipe-1.1.16 Animal Social Network Inference and Permutations for Ecologistsassertive-0.3-6 Readable Check Functions to Ensure Code Integrityassertive.base-0.0-9 A Lightweight Core of the ‘assertive’ Packageassertive.code-0.0-3 Assertions to Check Properties of Codeassertive.data-0.0-3 Assertions to Check Properties of Dataassertive.data.uk-0.0-2 Assertions to Check Properties of Stringsassertive.data.us-0.0-2 Assertions to Check Properties of Stringsassertive.datetimes-0.0-3 Assertions to Check Properties of Dates and Timesassertive.files-0.0-2 Assertions to Check Properties of Filesassertive.matrices-0.0-2 Assertions to Check Properties of Matricesassertive.models-0.0-2 Assertions to Check Properties of Modelsassertive.numbers-0.0-2 Assertions to Check Properties of Numbersassertive.properties-0.0-4 Assertions to Check Properties of Variablesassertive.reflection-0.0-5 Assertions for Checking the State of Rassertive.sets-0.0-3 Assertions to Check Properties of Setsassertive.strings-0.0-3 Assertions to Check Properties of Stringsassertive.types-0.0-3 Assertions to Check Types of Variablesassertthat-0.2.1 Easy Pre and Post Assertionsaudio-0.1-7 Audio Interface for Raws-2.5-1 Adaptive Weights Smoothingaws.ec2metadata-0.2.0 Get EC2 Instance Metadataaws.s3-0.3.21 ‘AWS S3’ Client Packageaws.signature-0.6.0 Amazon Web Services Request SignaturesawsMethods-1.1-1 Class and Methods Definitions for Packages ‘aws’, ‘adimpro’,
‘fmri’, ‘dwi’babelgene-21.4 Gene Orthologs for Model Organisms in a Tidy Data Formatbackports-1.2.1 Reimplementations of Functions Introduced Since R-3.0.0bacr-1.0.1 Bayesian Adjustment for Confoundingbamsignals-1.24.0 Extract read count signals from bam filesbartMachine-1.2.6 Bayesian Additive Regression TreesbartMachineJARs-1.1 bartMachine JARsbase built in
base64-2.0 Base64 Encoder and Decoderbase64enc-0.1-3 Tools for base64 encodingbase64url-1.4 Fast and URL-Safe Base64 Encoder and Decoderbatchmeans-1.0-4 Consistent Batch Means Estimation of Monte Carlo Standard Errorsbatchtools-0.9.15 Tools for Computation on Batch SystemsbaySeq-2.26.0 Empirical Bayesian analysis of patterns of differential expression in count databayesm-3.1-4 Bayesian Inference for Marketing/Micro-Econometricsbayesplot-1.8.1 Plotting for Bayesian Modelsbbmle-1.0.24 Tools for General Maximum Likelihood Estimationbdsmatrix-1.3-4 Routines for Block Diagonal Symmetric Matricesbeachmat-2.8.1 Compiling Bioconductor to Handle Each Matrix Typebeanplot-1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin<U+000a>Plot)beeswarm-0.4.0 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
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