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
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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
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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
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‘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
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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]
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Ordered Observations)
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