Known Issues
Package List
ADGofTest-0.3 Anderson-Darling GoF testALDEx2-1.32.0 Analysis Of Differential Abundance Taking Sample Variation Into AccountALL-1.42.0 A data packageASCAT 3.1.2 [CRAN]
AgiMicroRna-2.50.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAnnotationDbi-1.62.2 Manipulation of SQLite-based annotations in BioconductorAnnotationFilter-1.24.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.42.2 Tools for building SQLite-based annotation data packagesAnnotationHub-3.8.0 Client to access AnnotationHub resourcesArchR 1.0.2 [CRAN]
BDgraph-2.72 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMCBSgenome-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 ExplorationBiasedUrn-2.0.10 Biased Urn Model DistributionsBiobase-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 OptimizationCairo-1.6-0 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-2.66.0 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 dataDESeq2-1.40.2 Differential gene expression analysis based on the negative binomial distributionDEoptimR-1.0-14 Differential Evolution Optimization in Pure RDNAcopy-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 RDT-0.28 A Wrapper of the JavaScript Library ‘DataTables’DelayedArray-0.26.6 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’ ObjectsDeriv-4.1.3 Symbolic DifferentiationDiffBind-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-2.4.0 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 probesFNN-1.1.3.2 Fast Nearest Neighbor Search Algorithms and ApplicationsFlowSOM-2.8.0 Using self-organizing maps for visualization and interpretation of cytometry dataFormula-1.2-5 Extended Model FormulasGENESIS-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)GGally-2.1.2 Extension to ‘ggplot2’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 microarraysGSA-1.03.2 Gene Set AnalysisGSEABase-1.62.0 Gene set enrichment data structures and methodsGSVA-1.48.2 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-1.36.1 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-1.52.1 Conveniently import and query gene modelsGenomicFiles-1.36.0 Distributed computing by file or by rangeGenomicRanges-1.52.0 Representation and manipulation of genomic intervalsGetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable InterpolationGlimma-2.10.0 Interactive HTML graphicsGlobalOptions-0.1.2 Generate Functions to Get or Set Global OptionsGmisc-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 HaplotypesHmisc-5.1-0 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-1.28.0 Independent Hypothesis WeightingIRanges-2.34.1 Foundation of integer range manipulation in BioconductorIRdisplay-1.1 ‘Jupyter’ Display MachineryIlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arraysInteractionSet-1.28.1 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-2.35 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
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ModelsRNASeqPower-1.40.0 Sample size for RNAseq studiesROCR-1.0-11 Visualizing the Performance of Scoring ClassifiersRPostgreSQL-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 buffersRSQLite-2.3.1 SQLite Interface for RRSclient-0.7-9 Client for RserveRSpectra-0.16-1 Solvers for Large-Scale Eigenvalue and SVD ProblemsRVenn-1.1.0 Set Operations for Many SetsRaggedExperiment-1.24.0 Representation of Sparse Experiments and Assays Across SamplesRcppAnnoy-0.0.21 ‘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 LibrariesRcppProgress-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”RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG
ImplementationsRdpack-2.4 Update and Manipulate Rd Documentation ObjectsRdsdp-1.0.5.2.1 R Interface to DSDP Semidefinite Programming LibraryReportingTools-2.39.0 Tools for making reports in various formatsRfast-2.0.8 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’RhpcBLASctl-0.23-42 Control the Number of Threads on ‘BLAS’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’ ServerRmpfr-0.9-2 R MPFR - Multiple Precision Floating-Point ReliableRmpi-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 dataRtsne-0.16 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
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