Known Issues
Package List
ALDEx2-1.38.0 Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountALL 1.46.0 Package Not Found
AgiMicroRna-2.56.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAnnotationDbi-1.68.0 Manipulation of SQLite-based annotations in BioconductorAnnotationFilter-1.30.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.48.0 Tools for building SQLite-based annotation data packagesAnnotationHub-3.14.0 Client to access AnnotationHub resourcesArchR 1.0.2 Package Not Found
BSgenome-1.74.0 Software infrastructure for efficient representation of full genomes and their SNPsBSgenome.Hsapiens.UCSC.hg19 1.4.3 Package Not Found
Bhat-0.9-12 General Likelihood ExplorationBiobase-2.66.0 Biobase: Base functions for BioconductorBiocBaseUtils-1.8.0 General utility functions for developing Bioconductor packagesBiocFileCache-2.14.0 Manage Files Across SessionsBiocGenerics-0.52.0 S4 generic functions used in BioconductorBiocIO-1.16.0 Standard Input and Output for Bioconductor PackagesBiocManager-1.30.25 Access the Bioconductor Project Package RepositoryBiocNeighbors-2.0.1 Nearest Neighbor Detection for Bioconductor PackagesBiocParallel-1.40.0 Bioconductor facilities for parallel evaluationBiocSingular-1.22.0 Singular Value Decomposition for Bioconductor PackagesBiocStyle-2.34.0 Standard styles for vignettes and other Bioconductor documentsBiocVersion-3.20.0 Set the appropriate version of Bioconductor packagesBiostrings-2.74.1 Efficient manipulation of biological stringsBivarP-1.0 Estimating the Parameters of Some Bivariate DistributionsBolstad-0.2.42 Functions for Elementary Bayesian InferenceBolstad2-1.0-29 Bolstad FunctionsBradleyTerry2-1.1-2 Bradley-Terry ModelsCATALYST-1.30.2 Cytometry dATa anALYSis ToolsCGHbase-1.66.0 CGHbase: Base functions and classes for arrayCGH data analysis.CLONETv2-2.2.1 Clonality Estimates in TumorCMA-1.64.0 Synthesis of microarray-based classificationCNEr-1.42.0 CNE Detection and VisualizationCOMPASS-1.44.0 Combinatorial Polyfunctionality Analysis of Single CellsCaSpER v2.0 Package Not Found
Category-2.72.0 Category AnalysisChIPQC-1.42.0 Quality metrics for ChIPseq dataChIPpeakAnno-3.40.0 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-1.42.1 ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationComplexHeatmap-2.22.0 Make Complex HeatmapsConsensusClusterPlus-1.70.0 ConsensusClusterPlusCytoML-2.18.2 A GatingML Interface for Cross Platform Cytometry Data SharingDAAG-1.25.6 Data Analysis and Graphics Data and FunctionsDECIPHER-3.2.0 Tools for curating, analyzing, and manipulating biological sequencesDEGseq-1.60.0 Identify Differentially Expressed Genes from RNA-seq dataDESeq2-1.46.0 Differential gene expression analysis based on the negative binomial distributionDNAcopy-1.80.0 DNA Copy Number Data AnalysisDO.db 2.9 Package Not Found
DOSE-4.0.0 Disease Ontology Semantic and Enrichment analysisDOT-0.1 Render and Export DOT Graphs in RDelayedArray-0.32.0 A unified framework for working transparently with on-disk and in-memory array-like datasetsDelayedMatrixStats-1.28.1 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ ObjectsDiceDesign-1.10 Designs of Computer ExperimentsDiffBind-3.16.0 Differential Binding Analysis of ChIP-Seq Peak DataDirichletMultinomial-1.48.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataDynDoc-1.84.0 Dynamic document toolsEBImage-4.48.0 Image processing and analysis toolbox for REpiModel-2.5.0 Mathematical Modeling of Infectious Disease DynamicsExperimentHub-2.14.0 Client to access ExperimentHub resourcesFDb.InfiniumMethylation.hg19 2.2.0 Package Not Found
FlowSOM-2.14.0 Using self-organizing maps for visualization and interpretation of cytometry dataGEOquery-2.74.0 Get data from NCBI Gene Expression Omnibus (GEO)GO.db 3.19.1 Package Not Found
GOSemSim-2.32.0 GO-terms Semantic Similarity MeasuresGOstats-2.72.0 Tools for manipulating GO and microarraysGPfit-1.0-8 Gaussian Processes ModelingGSEABase-1.68.0 Gene set enrichment data structures and methodsGSVA-2.0.5 Gene Set Variation Analysis for Microarray and RNA-Seq DataGWASExactHW-1.2 Exact Hardy-Weinburg Testing for Genome Wide Association StudiesGWASTools-1.52.0 Tools for Genome Wide Association StudiesGenomeInfoDb-1.42.3 Utilities for manipulating chromosome names, including modifying them to follow a particular naming styleGenomeInfoDbData 1.2.12 Package Not Found
GenomicAlignments-1.42.0 Representation and manipulation of short genomic alignmentsGenomicFeatures-1.58.0 Query the gene models of a given organism/assemblyGenomicFiles-1.42.0 Distributed computing by file or by rangeGenomicRanges-1.58.0 Representation and manipulation of genomic intervalsGlimma-2.16.0 Interactive visualizations for gene expression analysisGmisc-3.0.3 Descriptive Statistics, Transition Plots, and MoreGreyListChIP-1.38.0 Grey Lists – Mask Artefact Regions Based on ChIP InputsGviz-1.50.0 Plotting data and annotation information along genomic coordinatesHDF5Array-1.34.0 HDF5 datasets as array-like objects in RHDO.db 0.99.1 Package Not Found
HMMcopy-1.48.0 Copy number prediction with correction for GC and mappability bias for HTS dataHSMMSingleCell 1.24.0 Package Not Found
HaploSim-1.8.4.2 Functions to Simulate HaplotypesHomo.sapiens 1.3.1 Package Not Found
IHW-1.34.0 Independent Hypothesis WeightingIRanges-2.40.1 Foundation of integer range manipulation in BioconductorIRdisplay-1.1 ‘Jupyter’ Display MachineryIlluminaHumanMethylation450kmanifest 0.4.0 Package Not Found
InteractionSet-1.34.0 Base Classes for Storing Genomic Interaction DataKEGGREST-1.46.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)KEGGgraph-1.66.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorLogicReg-1.6.6 Logic RegressionLymphoSeq-1.34.0 Analyze high-throughput sequencing of T and B cell receptorsLymphoSeqDB 0.99.2 Package Not Found
MAGeCKFlute-2.9.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic ScreensMAST-1.32.0 Model-based Analysis of Single Cell TranscriptomicsMCMCglmm-2.36 MCMC Generalised Linear Mixed ModelsMPV-1.64 Data Sets from Montgomery, Peck and ViningMatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
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PICS-2.50.0 Probabilistic inference of ChIP-seqPolynomF-2.0-8 Polynomials in RProtGenerics-1.38.0 Generic infrastructure for Bioconductor mass spectrometry packagesQUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix EstimationR2jags-0.8-9 Using R to Run ‘JAGS’RBGL-1.82.0 An interface to the BOOST graph libraryREDCapR-1.4.0 Interaction Between R and REDCapRLRsim-3.1-8 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
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RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG
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MatricesTitanCNA-1.44.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumoursTxDb.Celegans.UCSC.ce6.ensGene 3.2.2 Package Not Found
TxDb.Dmelanogaster.UCSC.dm3.ensGene 3.2.2 Package Not Found
TxDb.Hsapiens.UCSC.hg18.knownGene 3.2.2 Package Not Found
TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2 Package Not Found
TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0 Package Not Found
TxDb.Mmusculus.UCSC.mm9.knownGene 3.2.2 Package Not Found
TxDb.Rnorvegicus.UCSC.rn4.ensGene 3.2.2 Package Not Found
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Compositional Data Setszeallot-0.1.0 Multiple, Unpacking, and Destructuring Assignmentzellkonverter-1.16.0 Conversion Between scRNA-seq Objectszip-2.3.1 Cross-Platform ‘zip’ Compressionzlibbioc-1.52.0 An R packaged zlib-1.2.5zoo-1.8-12 S3 Infrastructure for Regular and Irregular Time Series (Z’s
Ordered Observations)