Known Issues
Package List
ALDEx2-1.30.0 Analysis Of Differential Abundance Taking Sample Variation Into AccountALL-1.40.0 A data packageASCAT 2.5.2 [CRAN]
AgiMicroRna-2.48.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAnnotationDbi-1.60.0 Manipulation of SQLite-based annotations in BioconductorAnnotationFilter-1.22.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.40.0 Tools for building SQLite-based annotation data packagesAnnotationHub-3.6.0 Client to access AnnotationHub resourcesArchR 1.0.1 [CRAN]
BSgenome-1.66.1 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-2.58.0 Biobase: Base functions for BioconductorBiocFileCache-2.6.0 Manage Files Across SessionsBiocGenerics-0.44.0 S4 generic functions used in BioconductorBiocIO-1.8.0 Standard Input and Output for Bioconductor PackagesBiocManager-1.30.19 Access the Bioconductor Project Package RepositoryBiocNeighbors-1.16.0 Nearest Neighbor Detection for Bioconductor PackagesBiocParallel-1.32.1 Bioconductor facilities for parallel evaluationBiocSingular-1.14.0 Singular Value Decomposition for Bioconductor PackagesBiocStyle-2.26.0 Standard styles for vignettes and other Bioconductor documentsBiocVersion-3.16.0 Set the appropriate version of Bioconductor packagesBiostrings-2.66.0 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-1.22.0 Cytometry dATa anALYSis ToolsCGHbase-1.58.0 CGHbase: Base functions and classes for arrayCGH data analysis.CLONETv2-2.2.1 Clonality Estimates in TumorCMA-1.56.0 Synthesis of microarray-based classificationCNEr-1.34.0 CNE Detection and VisualizationCOMPASS-1.36.0 Combinatorial Polyfunctionality Analysis of Single CellsCVXR-1.0-11 Disciplined Convex OptimizationCategory-2.64.0 Category AnalysisChIPpeakAnno-3.32.0 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome rangesChIPseeker-1.34.0 ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationComplexHeatmap-2.14.0 Make Complex HeatmapsConsensusClusterPlus-1.62.0 ConsensusClusterPlusCytoML-2.10.0 A GatingML Interface for Cross Platform Cytometry Data SharingDAAG-1.25.4 Data Analysis and Graphics Data and FunctionsDECIPHER-2.26.0 Tools for curating, analyzing, and manipulating biological sequencesDEGseq-1.52.0 Identify Differentially Expressed Genes from RNA-seq dataDESeq2-1.38.0 Differential gene expression analysis based on the negative binomial distributionDNAcopy-1.72.0 DNA copy number data analysisDO.db-2.9 A set of annotation maps describing the entire Disease OntologyDOSE-3.24.1 Disease Ontology Semantic and Enrichment analysisDOT-0.1 Render and Export DOT Graphs in RDelayedArray-0.24.0 A unified framework for working transparently with on-disk and in-memory array-like datasetsDelayedMatrixStats-1.20.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ ObjectsDiceDesign-1.9 Designs of Computer ExperimentsDiffBind-3.8.1 Differential Binding Analysis of ChIP-Seq Peak DataDirichletMultinomial-1.40.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataDynDoc-1.76.0 Dynamic document toolsEBImage-4.40.0 Image processing and analysis toolbox for RECOSolveR-0.5.4 Embedded Conic Solver in REpiModel-2.3.1 Mathematical Modeling of Infectious Disease DynamicsExperimentHub-2.6.0 Client to access ExperimentHub resourcesFDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probesFlowSOM-2.6.0 Using self-organizing maps for visualization and interpretation of cytometry dataGENESIS-2.28.0 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessGEOquery-2.66.0 Get data from NCBI Gene Expression Omnibus (GEO)GO.db-3.16.0 A set of annotation maps describing the entire Gene OntologyGOSemSim-2.24.0 GO-terms Semantic Similarity MeasuresGOstats-2.64.0 Tools for manipulating GO and microarraysGPfit-1.0-8 Gaussian Processes ModelingGSEABase-1.60.0 Gene set enrichment data structures and methodsGSVA-1.46.0 Gene Set Variation Analysis for microarray and RNA-seq dataGWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association StudiesGWASTools-1.44.0 Tools for Genome Wide Association StudiesGenomeGraphs 1.46.0 [CRAN]
GenomeInfoDb-1.34.3 Utilities for manipulating chromosome names, including modifying them to follow a particular naming styleGenomeInfoDbData-1.2.9 Species and taxonomy ID look up tables used by GenomeInfoDbGenomicAlignments-1.34.0 Representation and manipulation of short genomic alignmentsGenomicFeatures-1.50.2 Conveniently import and query gene modelsGenomicFiles-1.34.0 Distributed computing by file or by rangeGenomicRanges-1.50.1 Representation and manipulation of genomic intervalsGlimma-2.8.0 Interactive HTML graphicsGmisc-3.0.0 Descriptive Statistics, Transition Plots, and MoreGreyListChIP-1.30.0 Grey Lists – Mask Artefact Regions Based on ChIP InputsGviz-1.42.0 Plotting data and annotation information along genomic coordinatesHDF5Array-1.26.0 HDF5 backend for DelayedArray objectsHDO.db-0.99.1 A set of annotation maps describing the entire Human Disease OntologyHMMcopy-1.40.0 Copy number prediction with correction for GC and mappability bias for HTS dataHSMMSingleCell-1.18.0 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-1.26.0 Independent Hypothesis WeightingIRanges-2.32.0 Foundation of integer range manipulation in BioconductorIRdisplay-1.1 ‘Jupyter’ Display MachineryIlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arraysInteractionSet-1.26.0 Base Classes for Storing Genomic Interaction DataKEGGREST-1.38.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)KEGGgraph-1.58.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorLogicReg-1.6.5 Logic RegressionLymphoSeq-1.26.0 Analyze high-throughput sequencing of T and B cell receptorsLymphoSeqDB-0.99.2 LymphoSeq annotation databasesMAGeCKFlute-2.2.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic ScreensMAST-1.24.0 Model-based Analysis of Single Cell TranscriptomicsMCMCglmm-2.34 MCMC Generalised Linear Mixed ModelsMPV-1.59 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-1.10.0 S4 Generic Summary Statistic Functions that Operate on Matrix-Like ObjectsMfuzz-2.58.0 Soft clustering of time series gene expression dataNADA-1.6-1.1 Nondetects and Data Analysis for Environmental DataNOISeq-2.42.0 Exploratory analysis and differential expression for RNA-seq dataOrganismDbi-1.40.0 Software to enable the smooth interfacing of different database packagesPBSddesolve-1.13.1 Solver for Delay Differential EquationsPFAM.db-3.16.0 A set of protein ID mappings for PFAMPICS-2.42.0 Probabilistic inference of ChIP-seqPolynomF-2.0-5 Polynomials in RProtGenerics-1.30.0 Generic infrastructure for Bioconductor mass spectrometry packagesQUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix EstimationR2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’R2jags-0.7-1 Using R to Run ‘JAGS’RBGL-1.74.0 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-1.38.0 Sample size for RNAseq studiesRNifti-1.4.3 Fast R and C++ Access to NIfTI ImagesRPostgreSQL-0.7-4 R Interface to the ‘PostgreSQL’ Database SystemRPresto-1.4.0 DBI Connector to PrestoRProtoBufLib-2.10.0 C++ headers and static libraries of Protocol buffersRSclient-0.7-8 Client for RserveRVenn-1.1.0 Set Operations for Many SetsRcppAnnoy-0.0.20 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
NeighborsRcppCCTZ-0.2.12 ‘Rcpp’ Bindings for the ‘CCTZ’ LibraryRcppDate-0.0.3 ‘date’ C++ Header Library for Date and Time FunctionalityRcppHNSW-0.4.1 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest
NeighborsRcppML-0.3.7 Rcpp Machine Learning LibraryRcppNumerical-0.4-0 ‘Rcpp’ Integration for Numerical Computing LibrariesRcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG
ImplementationsRdsdp-1.0.5.2 R Interface to DSDP Semidefinite Programming LibraryReportingTools-2.38.0 Tools for making reports in various formatsRfast-2.0.6 A Collection of Efficient and Extremely Fast R FunctionsRgraphviz-2.42.0 Provides plotting capabilities for R graph objectsRhdf5lib-1.20.0 hdf5 library as an R packageRhpc-0.21-247 Permits *apply() Style Dispatch for ‘HPC’Rhtslib-2.0.0 HTSlib high-throughput sequencing library as an R packageRingo-1.62.0 R Investigation of ChIP-chip OligoarraysRlabkey-2.9.0 Data Exchange Between R and ‘LabKey’ ServerRsamtools-2.14.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importRsubread-2.12.0 Mapping, quantification and variant analysis of sequencing dataS4Vectors-0.36.0 Foundation of vector-like and list-like containers in BioconductorSNPRelate-1.32.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)SNPassoc-2.0-17 SNPs-Based Whole Genome Association StudiesSPIA-2.50.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsScaledMatrix-1.6.0 Creating a DelayedMatrix of Scaled and Centered ValuesSemiPar-1.0-4.2 Semiparametic RegressionSeqArray-1.38.0 Data Management of Large-Scale Whole-Genome Sequence Variant CallsSeqVarTools-1.36.0 Tools for variant dataShortRead-1.56.0 FASTQ input and manipulationSingleCellExperiment-1.20.0 S4 Classes for Single Cell DataSummarizedExperiment-1.28.0 SummarizedExperiment containerTFBSTools-1.36.0 Software Package for Transcription Factor Binding Site (TFBS) AnalysisTFMPvalue-0.0.9 Efficient and Accurate P-Value Computation for Position Weight
MatricesTitanCNA-1.36.0 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-1.44.0 Annotation of Genetic VariantsWrench-1.16.0 Wrench normalization for sparse count dataXVector-0.38.0 Foundation of external vector representation and manipulation in Bioconductoraffxparser-1.70.0 Affymetrix File Parsing SDKaffy-1.76.0 Methods for Affymetrix Oligonucleotide Arraysaffycoretools-1.70.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChipsaffyio-1.68.0 Tools for parsing Affymetrix data filesalr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Editionamap-0.8-19 Another Multidimensional Analysis Packageannaffy-1.70.0 Annotation tools for Affymetrix biological metadataannotate-1.76.0 Annotation for microarraysapeglm-1.20.0 Approximate posterior estimation for GLM coefficientsaplot-0.1.8 Decorate a ‘ggplot’ with Associated Informationargparser-0.7.1 Command-Line Argument Parserarsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical
Summariesarules-1.7-5 Mining Association Rules and Frequent Itemsetsash-1.0-15 David Scott’s ASH Routinesashr-2.2-54 Methods for Adaptive Shrinkage, using Empirical Bayesaws.ec2metadata-0.2.0 Get EC2 Instance Metadataaws.s3-0.3.21 ‘AWS S3’ Client Packageaws.signature-0.6.0 Amazon Web Services Request Signaturesbabelgene-22.9 Gene Orthologs for Model Organisms in a Tidy Data Formatbamsignals-1.30.0 Extract read count signals from bam filesbase64url-1.4 Fast and URL-Safe Base64 Encoder and Decoderbatchtools-0.9.15 Tools for Computation on Batch SystemsbaySeq-2.31.0 Empirical Bayesian analysis of patterns of differential expression in count databeachmat-2.14.0 Compiling Bioconductor to Handle Each Matrix Typebenchmark-0.3-6 Benchmark Experiments Toolboxbezier-1.1.2 Toolkit for Bezier Curves and Splinesbiglm-0.9-2.1 Bounded Memory Linear and Generalized Linear ModelsbiomaRt-2.54.0 Interface to BioMart databases (i.e. Ensembl)biomformat-1.26.0 An interface package for the BIOM file formatbiovizBase-1.46.0 Basic graphic utilities for visualization of genomic data.bookdown-0.30 Authoring Books and Technical Documents with R Markdownbreakaway-4.8.2 Species Richness Estimation and Modelingbumphunter-1.40.0 Bump Huntercatdata-1.2.2 Categorical Datachipseq-1.48.0 chipseq: A package for analyzing chipseq datachromVAR-1.20.0 Chromatin Variation Across RegionsclusterProfiler-4.6.0 A universal enrichment tool for interpreting omics datacolorRamps-2.3.1 Builds Color Tablescompare-0.2-6 Comparing Objects for Differencesconfig-0.3.1 Manage Environment Specific Configuration Valuesconflicted-1.1.0 An Alternative Conflict Resolution Strategycopynumber-1.38.0 Segmentation of single- and multi-track copy number data by penalized least squares regression.cummeRbund-2.40.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.curry-0.1.1 Partial Function Application with %<%, %-<%, and %><%cyclocomp-1.1.0 Cyclomatic Complexity of R Codecytolib-2.10.0 C++ infrastructure for representing and interacting with the gated cytometry datadada2-1.26.0 Accurate, high-resolution sample inference from amplicon sequencing datadbscan-1.1-11 Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related Algorithmsdegreenet-1.3-3 Models for Skewed Count Distributions Relevant to Networksdepmap-1.12.0 Cancer Dependency Map Data Packagederfinder-1.32.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approachderfinderHelper-1.32.0 derfinder helper packagedescr-1.1.5 Descriptive Statisticsdfoptim-2020.10-1 Derivative-Free Optimizationdials-1.1.0 Tools for Creating Tuning Parameter Valuesdiamonds-1.0-5 Analysis and sampling grids from diamond partitionsdiffusionMap-1.2.0 Diffusion MapdoBy-4.6.14 Groupwise Statistics, LSmeans, Linear Estimates, UtilitiesdoMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Packagedqrng-0.3.0 Fast Pseudo Random Number Generatorsdrc-3.0-1 Analysis of Dose-Response CurvesedgeR-3.40.0 Empirical Analysis of Digital Gene Expression Data in Relasticnet-1.3 Elastic-Net for Sparse Estimation and Sparse PCAenrichplot-1.18.0 Visualization of Functional Enrichment Resultensembldb-2.22.0 Utilities to create and use Ensembl-based annotation databasesepitools-0.5-10.1 Epidemiology Toolsetrunct-0.1 Computes Moments of Univariate Truncated t Distributioneuropepmc-0.4.1 R Interface to the Europe PubMed Central RESTful Web ServicefANCOVA-0.6-1 Nonparametric Analysis of Covariancefaraway-1.0.8 Functions and Datasets for Books by Julian Farawayfastseg-1.44.0 fastseg - a fast segmentation algorithmfasttime-1.1-0 Fast Utility Function for Time Parsing and Conversionfda-6.0.5 Functional Data Analysisfds-1.8 Functional Data Setsfgsea-1.24.0 Fast Gene Set Enrichment Analysisfilelock-1.0.2 Portable File Lockingfit.models-0.64 Compare Fitted Modelsfloat-0.3-0 32-Bit FloatsflowClust-3.36.0 Clustering for Flow CytometryflowCore-2.10.0 flowCore: Basic structures for flow cytometry dataflowStats-4.10.0 Statistical methods for the analysis of flow cytometry dataflowViz-1.62.0 Visualization for flow cytometryflowWorkspace-4.10.0 Infrastructure for representing and interacting with gated and ungated cytometry data sets.forestplot-3.1.0 Advanced Forest Plot Using ‘grid’ Graphicsforge-0.2.0 Casting Values into Shapefts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)gage-2.48.0 Generally Applicable Gene-set Enrichment for Pathway Analysisgcrma-2.70.0 Background Adjustment Using Sequence Informationgdsfmt-1.34.0 gdtools-0.2.4 Utilities for Graphical RenderinggeneLenDataBase-1.34.0 Lengths of mRNA transcripts for a number of genomesgenefilter-1.80.0 genefilter: methods for filtering genes from high-throughput experimentsgeneplotter-1.76.0 Graphics related functions for BioconductorggVennDiagram-1.2.2 A ‘ggplot2’ Implement of Venn Diagramggbio-1.46.0 Visualization tools for genomic dataggcyto-1.26.0 Visualize Cytometry data with ggplotggdendro-0.1.23 Create Dendrograms and Tree Diagrams Using ‘ggplot2’ggfun-0.0.8 Miscellaneous Functions for ‘ggplot2’ggnewscale-0.4.8 Multiple Fill and Colour Scales in ‘ggplot2’ggplotify-0.1.0 Convert Plot to ‘grob’ or ‘ggplot’ Objectggpointdensity-0.1.0 A Cross Between a 2D Density Plot and a Scatter Plotggrastr-1.0.1 Rasterize Layers for ‘ggplot2’ggthemes-4.2.4 Extra Themes, Scales and Geoms for ‘ggplot2’ggtree-3.6.2 an R package for visualization of tree and annotation dataglmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox
Proportional Hazards Modelgoseq-1.50.0 Gene Ontology analyser for RNA-seq and other length biased datagraph-1.76.0 graph: A package to handle graph data structuresgridGraphics-0.5-1 Redraw Base Graphics Using ‘grid’ Graphicsgson-0.0.9 Base Class and Methods for ‘gson’ Formatgsubfn-0.7 Utilities for Strings and Function Argumentshapassoc-1.2-9 Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithmhaplo.stats-1.8.9 Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguoushdrcde-3.4 Highest Density Regions and Conditional Density Estimationhgu133plus2.db-3.13.0 Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)hopach-2.58.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)hypergate-0.8.3 Machine Learning of Hyperrectangular Gating Strategies for
High-Dimensional Cytometryigraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Packageilluminaio-0.40.0 Parsing Illumina Microarray Output Filesimpute-1.72.1 impute: Imputation for microarray datainfer-1.0.3 Tidy Statistical Inferenceinferference-1.0.2 Methods for Causal Inference with InterferenceinteractiveDisplayBase-1.36.0 Base package for enabling powerful shiny web displays of Bioconductor objectsinvgamma-1.1 The Inverse Gamma Distributioniotools-0.3-2 I/O Tools for Streamingits-1.1.8 Irregular Time SerieskaryoploteR-1.24.0 Plot customizable linear genomes displaying arbitrary datakeyring-1.3.1 Access the System Credential Store from Rkin.cohort-0.7 Analysis of Kin-Cohort Studieskinship2-1.9.6 Pedigree Functionsknockoff-0.3.6 The Knockoff Filter for Controlled Variable Selectionkyotil-2022.9-17 Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studieslasso2-1.2-22 L1 Constrained Estimation aka `lasso’latentnet-2.10.6 Latent Position and Cluster Models for Statistical Networkslgr-0.4.4 A Fully Featured Logging Frameworklimma-3.54.0 Linear Models for Microarray Datalintr-3.0.2 A ‘Linter’ for R Codelokern-1.1-9 Kernel Regression Smoothing with Local or Global Plug-in
Bandwidthlpridge-1.0-8 Local Polynomial (Ridge) Regressionlpsymphony-1.26.0 Symphony integer linear programming solver in Rlumi-2.50.0 BeadArray Specific Methods for Illumina Methylation and Expression MicroarraysmaSigPro-1.70.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Datamapdata-2.3.1 Extra Map Databasesmarray-1.76.0 Exploratory analysis for two-color spotted microarray datametagenomeSeq-1.40.0 Statistical analysis for sparse high-throughput sequencingmethylKit-1.24.0 DNA methylation analysis from high-throughput bisulfite sequencing resultsmethylumi-2.44.0 Handle Illumina methylation dataminfi-1.44.0 Analyze Illumina Infinium DNA methylation arraysmixOmics-6.22.0 Omics Data Integration Projectmixsqp-0.3-43 Sequential Quadratic Programming for Fast Maximum-Likelihood
Estimation of Mixture Proportionsmlapi-0.1.1 Abstract Classes for Building ‘scikit-learn’ Like APImodeldata-1.0.1 Data Sets Useful for Modeling Examplesmondate-0.10.02 Keep Track of Dates in Terms of Monthsmotifmatchr-1.20.0 Fast Motif Matching in Rmsa-1.30.0 Multiple Sequence Alignmentmsigdbr-7.5.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Formatmulttest-2.54.0 Resampling-based multiple hypothesis testingnanotime-0.3.7 Nanosecond-Resolution Time Support for RncdfFlow-2.44.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.ndtv-0.13.2 Network Dynamic Temporal Visualizationsnetworksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through
Sequential Importance Samplingnumbers-0.8-2 Number-Theoretic Functionsnws-1.7.0.1 R functions for NetWorkSpaces and Sleighodbc-1.3.3 Connect to ODBC Compatible Databases (using the DBI Interface)oligo-1.62.0 Preprocessing tools for oligonucleotide arraysoligoClasses-1.60.0 Classes for high-throughput arrays supported by oligo and crlmmopenCyto-2.10.0 Hierarchical Gating Pipeline for flow cytometry dataorg.Hs.eg.db-3.16.0 Genome wide annotation for Humanorg.Mm.eg.db-3.16.0 Genome wide annotation for Mouseoro.nifti-0.11.4 Rigorous - ‘NIfTI’ + ‘ANALYZE’ + ‘AFNI’ : Input / Outputosqp-0.6.0.7 Quadratic Programming Solver using the ‘OSQP’ Librarypack-0.1-1 Convert values to/from raw vectorsparsnip-1.0.3 A Common API to Modeling and Analysis Functionspartools-1.1.6 Tools for the ‘Parallel’ Packagepathview-1.38.0 a tool set for pathway based data integration and visualizationpbs-1.1 Periodic B SplinespcaMethods-1.90.0 A collection of PCA methodspdftools-3.3.2 Text Extraction, Rendering and Converting of PDF Documentspdist-1.2.1 Partitioned Distance Functionpedigree-1.4.2 Pedigree Functionspedigreemm-0.3-3 Pedigree-based mixed-effects modelsperm-1.0-0.2 Exact or Asymptotic Permutation Testsphyloseq-1.42.0 Handling and analysis of high-throughput microbiome census datapoisbinom-1.0.1 A Faster Implementation of the Poisson-Binomial Distributionpolyester-1.34.0 Simulate RNA-seq readspolyreg-0.8.0 Polynomial RegressionpoweRlaw-0.70.6 Analysis of Heavy Tailed Distributionspremessa 0.2.6 [CRAN]
preprocessCore-1.60.0 A collection of pre-processing functionspsychotools-0.7-2 Psychometric Modeling InfrastructureqdapRegex-0.7.5 Regular Expression Removal, Extraction, and Replacement Toolsqpdf-1.3.0 Split, Combine and Compress PDF Filesqtl-1.52 Tools for Analyzing QTL Experimentsquantoptr-0.1.3 Algorithms for Quantile- And Mean-Optimal Treatment Regimesquantsmooth-1.64.0 Quantile smoothing and genomic visualization of array dataqvalue-2.30.0 Q-value estimation for false discovery rate controlqvcalc-1.0.2 Quasi Variances for Factor Effects in Statistical Modelsr2d3-0.2.6 Interface to ‘D3’ VisualizationsrARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD ProblemsrGADEM-2.46.0 de novo motif discoveryrainbow-3.7 Bagplots, Boxplots and Rainbow Plots for Functional Datarbenchmark-1.0.0 Benchmarking routine for RrefGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from
‘Ensembl’ and ‘UCSC’ Genome Browsersrefund-0.1-28 Regression with Functional DataregioneR-1.30.0 Association analysis of genomic regions based on permutation testsregress-1.3-21 Gaussian Linear Models with Linear Covariance Structureregtools-1.7.0 Regression and Classification Toolsrelations-0.6-12 Data Structures and Algorithms for Relationsrelevent-1.1 Relational Event Modelsrepr-1.1.4 Serializable Representationsrestfulr-0.0.15 R Interface to RESTful Web Servicesrgenoud-5.9-0.3 R Version of GENetic Optimization Using Derivativesrhandsontable-0.3.8 Interface to the ‘Handsontable.js’ Libraryrhdf5-2.42.0 R Interface to HDF5rhdf5filters-1.10.0 HDF5 Compression Filtersrjags-4-13 Bayesian Graphical Models using MCMCrje-1.12.1 Miscellaneous Useful Functions for Statisticsrlist-0.4.6.2 A Toolbox for Non-Tabular Data Manipulationrsample-1.1.0 General Resampling Infrastructurerslurm-0.6.1 Submit R Calculations to a ‘Slurm’ Clusterrsparse-0.5.1 Statistical Learning on Sparse Matricesrstanarm-2.21.3 Bayesian Applied Regression Modeling via Stanrsvd-1.0.5 Randomized Singular Value Decompositionrtracklayer-1.58.0 R interface to genome annotation files and the UCSC genome browserrvcheck-0.2.1 R/Package Version Checkrzmq-0.9.8 R Bindings for ‘ZeroMQ’samr-3.0 SAM: Significance Analysis of Microarraysscater-1.26.1 Single-Cell Analysis Toolkit for Gene Expression Data in Rscattermore-0.8 Scatterplots with More Pointsscatterpie-0.1.8 Scatter Pie Plotschoolmath-0.4.1 Functions and Datasets for Math Used in Schoolscidb-3.0.0 An R Interface to SciDBscrime-1.3.5 Analysis of High-Dimensional Categorical Data Such as SNP Datascs-3.0-1 Splitting Conic Solverscuttle-1.8.0 Single-Cell RNA-Seq Analysis UtilitiesseqLogo-1.64.0 Sequence logos for DNA sequence alignmentsseqminer-8.4 Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into Rsequenza-3.0.0 Copy Number Estimation from Tumor Genome Sequencing Datasets-1.0-21 Sets, Generalized Sets, Customizable Sets and Intervalsshadowtext-0.1.2 Shadow Text Grob and LayershinyBS-0.61.1 Twitter Bootstrap Components for ShinyshinyFiles-0.9.3 A Server-Side File System Viewer for Shinyshinycssloaders-1.0.0 Add Loading Animations to a ‘shiny’ Output While It’s
Recalculatingsiggenes-1.72.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approachessitmo-2.0.2 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header
Filesslider-0.2.2 Sliding Window FunctionssnpStats-1.48.0 SnpMatrix and XSnpMatrix classes and methodssodium-1.2.1 A Modern and Easy-to-Use Crypto Librarysparklyr-1.7.8 R Interface to Apache SparksparseMatrixStats-1.10.0 Summary Statistics for Rows and Columns of Sparse Matricessqldf-0.4-11 Manipulate R Data Frames Using SQLsquash-1.0.9 Color-Based Plots for Multivariate Visualizationssgraph-1.14 Bayesian Graph Structure Learning using Spike-and-Slab Priorssva-3.46.0 Surrogate Variable AnalysissystemPipeR-2.4.0 systemPipeR: NGS workflow and report generation environmenttables-0.9.10 Formula-Driven Table GenerationtergmLite-2.6.1 Fast Simulation of Simple Temporal Exponential Random Graph
Modelstext2vec-0.6.2 Modern Text Mining Framework for Rtidymodels-1.0.0 Easily Install and Load the ‘Tidymodels’ Packagestidyposterior-1.0.0 Bayesian Analysis to Compare Models using Resampling Statisticstidypredict-0.4.9 Run Predictions Inside the Databasetidytree-0.4.1 A Tidy Tool for Phylogenetic Tree Data ManipulationtilingArray-1.76.0 Transcript mapping with high-density oligonucleotide tiling arraystimeSeries-4021.105 Financial Time Series Objects (Rmetrics)tkWidgets-1.76.0 R based tk widgetstreeio-1.22.0 Base Classes and Functions for Phylogenetic Tree Input and Outputtune-1.0.1 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-2.3.0 Perform Inference on Algorithm-Agnostic Variable Importancevsn-3.66.0 Variance stabilization and calibration for microarray datawarp-0.2.0 Group Dateswavethresh-4.7.1 Wavelets Statistics and Transformswebp-1.1.0 A New Format for Lossless and Lossy Image CompressionwidgetTools-1.76.0 Creates an interactive tcltk widgetworkflows-1.1.0 Modeling Workflowsworkflowsets-1.0.0 Create a Collection of ‘tidymodels’ WorkflowsxCell 1.1.0 [CRAN]
xmlparsedata-1.0.5 Parse Data of ‘R’ Code as an ‘XML’ Treeyardstick-1.1.0 Tidy Characterizations of Model Performanceyulab.utils-0.0.5 Supporting Functions for Packages Maintained by ‘YuLab-SMU’zCompositions-1.4.0-1 Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Setszlibbioc-1.44.0 An R packaged zlib-1.2.5
Edit this Page via GitHub Comment by Filing an Issue Have Questions? Ask them here.