Known Issues
Package List
ALDEx2-1.32.0 Analysis Of Differential Abundance Taking Sample Variation Into AccountALL-1.42.0 A data packageASCAT 2.5.2 [CRAN]
AgiMicroRna-2.50.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAnnotationDbi-1.62.1 Manipulation of SQLite-based annotations in BioconductorAnnotationFilter-1.24.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.42.0 Tools for building SQLite-based annotation data packagesAnnotationHub-3.8.0 Client to access AnnotationHub resourcesArchR 1.0.1 [CRAN]
BSgenome-1.68.0 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 ExplorationBiobase-2.60.0 Biobase: Base functions for BioconductorBiocFileCache-2.8.0 Manage Files Across SessionsBiocGenerics-0.46.0 S4 generic functions used in BioconductorBiocIO-1.10.0 Standard Input and Output for Bioconductor PackagesBiocManager-1.30.21 Access the Bioconductor Project Package RepositoryBiocNeighbors-1.18.0 Nearest Neighbor Detection for Bioconductor PackagesBiocParallel-1.34.2 Bioconductor facilities for parallel evaluationBiocSingular-1.16.0 Singular Value Decomposition for Bioconductor PackagesBiocStyle-2.28.0 Standard styles for vignettes and other Bioconductor documentsBiocVersion-3.17.1 Set the appropriate version of Bioconductor packagesBiostrings-2.68.1 Efficient manipulation of biological stringsBivarP-1.0 Estimating the Parameters of Some Bivariate DistributionsBolstad-0.2-41 Functions for Elementary Bayesian InferenceBolstad2-1.0-29 Bolstad FunctionsBradleyTerry2-1.1-2 Bradley-Terry ModelsCATALYST-1.24.0 Cytometry dATa anALYSis ToolsCGHbase-1.60.0 CGHbase: Base functions and classes for arrayCGH data analysis.CLONETv2-2.2.1 Clonality Estimates in TumorCMA-1.58.0 Synthesis of microarray-based classificationCNEr-1.36.0 CNE Detection and VisualizationCOMPASS-1.38.1 Combinatorial Polyfunctionality Analysis of Single CellsCVXR-1.0-11 Disciplined Convex OptimizationCategory-2.66.0 Category AnalysisChIPpeakAnno-3.34.1 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome rangesChIPseeker-1.36.0 ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationComplexHeatmap-2.16.0 Make Complex HeatmapsConsensusClusterPlus-1.64.0 ConsensusClusterPlusCytoML-2.12.0 A GatingML Interface for Cross Platform Cytometry Data SharingDAAG-1.25.4 Data Analysis and Graphics Data and FunctionsDECIPHER-2.28.0 Tools for curating, analyzing, and manipulating biological sequencesDEGseq-1.54.0 Identify Differentially Expressed Genes from RNA-seq dataDESeq2-1.40.1 Differential gene expression analysis based on the negative binomial distributionDNAcopy-1.74.1 DNA copy number data analysisDO.db-2.9 A set of annotation maps describing the entire Disease OntologyDOSE-3.26.1 Disease Ontology Semantic and Enrichment analysisDOT-0.1 Render and Export DOT Graphs in RDelayedArray-0.26.3 A unified framework for working transparently with on-disk and in-memory array-like datasetsDelayedMatrixStats-1.22.1 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ ObjectsDiceDesign-1.9 Designs of Computer ExperimentsDiffBind-3.10.0 Differential Binding Analysis of ChIP-Seq Peak DataDirichletMultinomial-1.42.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataDynDoc-1.78.0 Dynamic document toolsEBImage-4.42.0 Image processing and analysis toolbox for RECOSolveR-0.5.5 Embedded Conic Solver in REpiModel-2.3.2 Mathematical Modeling of Infectious Disease DynamicsExperimentHub-2.8.0 Client to access ExperimentHub resourcesFDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probesFlowSOM-2.8.0 Using self-organizing maps for visualization and interpretation of cytometry dataGENESIS-2.30.0 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessGEOquery-2.68.0 Get data from NCBI Gene Expression Omnibus (GEO)GO.db-3.17.0 A set of annotation maps describing the entire Gene OntologyGOSemSim-2.26.0 GO-terms Semantic Similarity MeasuresGOstats-2.66.0 Tools for manipulating GO and microarraysGPfit-1.0-8 Gaussian Processes ModelingGSEABase-1.62.0 Gene set enrichment data structures and methodsGSVA-1.48.1 Gene Set Variation Analysis for microarray and RNA-seq dataGWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association StudiesGWASTools-1.46.0 Tools for Genome Wide Association StudiesGenomeInfoDb-1.36.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming styleGenomeInfoDbData-1.2.10 Species and taxonomy ID look up tables used by GenomeInfoDbGenomicAlignments-1.36.0 Representation and manipulation of short genomic alignmentsGenomicFeatures-1.52.0 Conveniently import and query gene modelsGenomicFiles-1.36.0 Distributed computing by file or by rangeGenomicRanges-1.52.0 Representation and manipulation of genomic intervalsGlimma-2.10.0 Interactive HTML graphicsGmisc-3.0.2 Descriptive Statistics, Transition Plots, and MoreGreyListChIP-1.32.0 Grey Lists – Mask Artefact Regions Based on ChIP InputsGviz-1.44.0 Plotting data and annotation information along genomic coordinatesHDF5Array-1.28.1 HDF5 backend for DelayedArray objectsHDO.db-0.99.1 A set of annotation maps describing the entire Human Disease OntologyHMMcopy-1.42.0 Copy number prediction with correction for GC and mappability bias for HTS dataHSMMSingleCell-1.20.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)HaploSim-1.8.4.2 Functions to Simulate HaplotypesHomo.sapiens-1.3.1 Annotation package for the Homo.sapiens objectIHW-1.28.0 Independent Hypothesis WeightingIRanges-2.34.0 Foundation of integer range manipulation in BioconductorIRdisplay-1.1 ‘Jupyter’ Display MachineryIlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arraysInteractionSet-1.28.0 Base Classes for Storing Genomic Interaction DataKEGGREST-1.40.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)KEGGgraph-1.60.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorLogicReg-1.6.5 Logic RegressionLymphoSeq-1.28.0 Analyze high-throughput sequencing of T and B cell receptorsLymphoSeqDB-0.99.2 LymphoSeq annotation databasesMAGeCKFlute-2.4.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic ScreensMAST-1.26.0 Model-based Analysis of Single Cell TranscriptomicsMCMCglmm-2.34 MCMC Generalised Linear Mixed ModelsMPV-1.62 Data Sets from Montgomery, Peck and ViningMatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
OperationsMatrixExtra-0.1.13 Extra Methods for Sparse MatricesMatrixGenerics-1.12.2 S4 Generic Summary Statistic Functions that Operate on Matrix-Like ObjectsMfuzz-2.60.0 Soft clustering of time series gene expression dataNADA-1.6-1.1 Nondetects and Data Analysis for Environmental DataNOISeq-2.44.0 Exploratory analysis and differential expression for RNA-seq dataOrganismDbi-1.42.0 Software to enable the smooth interfacing of different database packagesPBSddesolve-1.13.3 Solver for Delay Differential EquationsPFAM.db-3.17.0 A set of protein ID mappings for PFAMPICS-2.44.0 Probabilistic inference of ChIP-seqPolynomF-2.0-5 Polynomials in RProtGenerics-1.32.0 Generic infrastructure for Bioconductor mass spectrometry packagesQUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix EstimationR2jags-0.7-1 Using R to Run ‘JAGS’RBGL-1.76.0 An interface to the BOOST graph libraryREDCapR-1.1.0 Interaction Between R and REDCapRLRsim-3.1-8 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
ModelsRNASeqPower-1.40.0 Sample size for RNAseq studiesRPostgreSQL-0.7-5 R Interface to the ‘PostgreSQL’ Database SystemRPresto-1.4.5 DBI Connector to PrestoRProtoBufLib-2.12.0 C++ headers and static libraries of Protocol buffersRSclient-0.7-9 Client for RserveRVenn-1.1.0 Set Operations for Many SetsRcppAnnoy-0.0.20 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
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NeighborsRcppML-0.3.7 Rcpp Machine Learning LibraryRcppNumerical-0.5-0 ‘Rcpp’ Integration for Numerical Computing LibrariesRcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG
ImplementationsRdsdp-1.0.5.2.1 R Interface to DSDP Semidefinite Programming LibraryReportingTools-2.39.0 Tools for making reports in various formatsRfast-2.0.7 A Collection of Efficient and Extremely Fast R FunctionsRgraphviz-2.44.0 Provides plotting capabilities for R graph objectsRhdf5lib-1.22.0 hdf5 library as an R packageRhpc-0.21-247 Permits *apply() Style Dispatch for ‘HPC’Rhtslib-2.2.0 HTSlib high-throughput sequencing library as an R packageRingo-1.64.0 R Investigation of ChIP-chip OligoarraysRlabkey-2.11.0 Data Exchange Between R and ‘LabKey’ ServerRmpi-0.7-1 Interface (Wrapper) to MPI (Message-Passing Interface)Rsamtools-2.16.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importRsubread-2.14.2 Mapping, quantification and variant analysis of sequencing dataS4Arrays-1.0.4 Foundation of array-like containers in BioconductorS4Vectors-0.38.1 Foundation of vector-like and list-like containers in BioconductorSNPRelate-1.34.1 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)SNPassoc-2.1-0 SNPs-Based Whole Genome Association StudiesSPIA-2.52.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsScaledMatrix-1.8.1 Creating a DelayedMatrix of Scaled and Centered ValuesSemiPar-1.0-4.2 Semiparametic RegressionSeqArray-1.40.1 Data Management of Large-Scale Whole-Genome Sequence Variant CallsSeqVarTools-1.38.0 Tools for variant dataShortRead-1.58.0 FASTQ input and manipulationSingleCellExperiment-1.22.0 S4 Classes for Single Cell DataSummarizedExperiment-1.30.2 SummarizedExperiment containerTFBSTools-1.38.0 Software Package for Transcription Factor Binding Site (TFBS) AnalysisTFMPvalue-0.0.9 Efficient and Accurate P-Value Computation for Position Weight
MatricesTitanCNA-1.38.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumoursTxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)VariantAnnotation-1.46.0 Annotation of Genetic VariantsWrench-1.18.0 Wrench normalization for sparse count dataXVector-0.40.0 Foundation of external vector representation and manipulation in Bioconductoraffxparser-1.72.0 Affymetrix File Parsing SDKaffy-1.78.0 Methods for Affymetrix Oligonucleotide Arraysaffycoretools-1.72.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChipsaffyio-1.70.0 Tools for parsing Affymetrix data filesalr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Editionamap-0.8-19 Another Multidimensional Analysis Packageannaffy-1.72.0 Annotation tools for Affymetrix biological metadataannotate-1.78.0 Annotation for microarraysapeglm-1.22.1 Approximate posterior estimation for GLM coefficientsargparser-0.7.1 Command-Line Argument Parserarsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical
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Modelstext2vec-0.6.3 Modern Text Mining Framework for Rtidymodels-1.1.0 Easily Install and Load the ‘Tidymodels’ Packagestidyposterior-1.0.0 Bayesian Analysis to Compare Models using Resampling Statisticstidypredict-0.5 Run Predictions Inside the DatabasetilingArray-1.78.0 Transcript mapping with high-density oligonucleotide tiling arraystimeSeries-4030.106 Financial Time Series Objects (Rmetrics)tkWidgets-1.78.0 R based tk widgetstreeio-1.24.1 Base Classes and Functions for Phylogenetic Tree Input and Outputtune-1.1.1 Tidy Tuning Toolsudunits2-0.13.2.1 Udunits-2 Bindings for Ruwot-0.1.14 The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reductionvenn-1.11 Draw Venn Diagramsvimp-2.3.1 Perform Inference on Algorithm-Agnostic Variable Importancevsn-3.68.0 Variance stabilization and calibration for microarray datawarp-0.2.0 Group Dateswavethresh-4.7.2 Wavelets Statistics and Transformswebp-1.1.0 A New Format for Lossless and Lossy Image CompressionwidgetTools-1.78.0 Creates an interactive tcltk widgetworkflows-1.1.3 Modeling Workflowsworkflowsets-1.0.1 Create a Collection of ‘tidymodels’ WorkflowsxCell 1.1.0 [CRAN]
xmlparsedata-1.0.5 Parse Data of ‘R’ Code as an ‘XML’ Treeyardstick-1.2.0 Tidy Characterizations of Model PerformancezCompositions-1.4.0-1 Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Setszlibbioc-1.46.0 An R packaged zlib-1.2.5