Known Issues
Package List
ADGofTest-0.3 Anderson-Darling GoF testAICcmodavg-2.3-1 Model Selection and Multimodel Inference Based on (Q)AIC(c)ALDEx2-1.28.0 Analysis Of Differential Abundance Taking Sample Variation Into AccountALL-1.38.0 A data packageASCAT 2.5.2
AUC-0.3.2 Threshold Independent Performance Measures for Probabilistic
ClassifiersAgiMicroRna-2.46.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAlgDesign-1.2.0 Algorithmic Experimental DesignAnalyzeFMRI-1.1-24 Functions for Analysis of fMRI Datasets Stored in the ANALYZE or
NIFTI FormatAnnotationDbi-1.58.0 Manipulation of SQLite-based annotations in BioconductorAnnotationFilter-1.20.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.38.0 Tools for building SQLite-based annotation data packagesAnnotationHub-3.4.0 Client to access AnnotationHub resourcesArchR 1.0.1
BB-2019.10-1 Solving and Optimizing Large-Scale Nonlinear SystemsBBmisc-1.12 Miscellaneous Helper Functions for B. BischlBCEE-1.3.0 The Bayesian Causal Effect Estimation AlgorithmBDgraph-2.66 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMCBH-1.78.0-0 Boost C++ Header FilesBIGL-1.6.5 Biochemically Intuitive Generalized Loewe ModelBMA-3.18.17 Bayesian Model AveragingBSgenome-1.64.0 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)BatchJobs-1.9 Batch Computing with RBayesPen-1.0 Bayesian Penalized Credible RegionsBayesianTools-0.1.7 General-Purpose MCMC and SMC Samplers and Tools for Bayesian
StatisticsBhat-0.9-10 General Likelihood ExplorationBiasedUrn-1.07 Biased Urn Model DistributionsBiobase-2.56.0 Biobase: Base functions for BioconductorBiocFileCache-2.4.0 Manage Files Across SessionsBiocGenerics-0.42.0 S4 generic functions used in BioconductorBiocIO-1.6.0 Standard Input and Output for Bioconductor PackagesBiocManager-1.30.17 Access the Bioconductor Project Package RepositoryBiocNeighbors-1.14.0 Nearest Neighbor Detection for Bioconductor PackagesBiocParallel-1.30.0 Bioconductor facilities for parallel evaluationBiocSingular-1.12.0 Singular Value Decomposition for Bioconductor PackagesBiocStyle-2.24.0 Standard styles for vignettes and other Bioconductor documentsBiocVersion-3.15.2 Set the appropriate version of Bioconductor packagesBiostrings-2.64.0 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 FunctionsBoruta-7.0.0 Wrapper Algorithm for All Relevant Feature SelectionBradleyTerry2-1.1-2 Bradley-Terry ModelsBrobdingnag-1.2-7 Very Large Numbers in RCATALYST-1.20.0 Cytometry dATa anALYSis ToolsCBPS-0.23 Covariate Balancing Propensity ScoreCGHbase-1.56.0 CGHbase: Base functions and classes for arrayCGH data analysis.CLONETv2-2.2.1 Clonality Estimates in TumorCMA-1.54.0 Synthesis of microarray-based classificationCNEr-1.32.0 CNE Detection and VisualizationCOMPASS-1.34.0 Combinatorial Polyfunctionality Analysis of Single CellsCVST-0.2-3 Fast Cross-Validation via Sequential TestingCVXR-1.0-10 Disciplined Convex OptimizationCairo-1.5-15 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-2.62.0 Category AnalysisChIPpeakAnno-3.30.0 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome rangesChIPseeker-1.32.0 ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationComICS-1.0.4 Computational Methods for Immune Cell-Type SubsetsCompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal VariablesComplexHeatmap-2.12.0 Make Complex HeatmapsConsensusClusterPlus-1.60.0 ConsensusClusterPlusCovSel-1.2.1 Model-Free Covariate SelectionCytoML-2.8.0 A GatingML Interface for Cross Platform Cytometry Data SharingDAAG-1.24 Data Analysis and Graphics Data and FunctionsDBI-1.1.2 R Database InterfaceDECIPHER-2.24.0 Tools for curating, analyzing, and manipulating biological sequencesDEGseq-1.50.0 Identify Differentially Expressed Genes from RNA-seq dataDESeq2-1.36.0 Differential gene expression analysis based on the negative binomial distributionDEoptim-2.2-6 Global Optimization by Differential EvolutionDEoptimR-1.0-11 Differential Evolution Optimization in Pure RDHARMa-0.4.5 Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression ModelsDMCfun-2.0.2 Diffusion Model of Conflict (DMC) in Reaction Time TasksDNAcopy-1.70.0 DNA copy number data analysisDO.db-2.9 A set of annotation maps describing the entire Disease OntologyDOSE-3.22.0 Disease Ontology Semantic and Enrichment analysisDOT-0.1 Render and Export DOT Graphs in RDRR-0.0.4 Dimensionality Reduction via RegressionDT-0.22 A Wrapper of the JavaScript Library ‘DataTables’DTRreg-1.7 DTR Estimation and Inference via G-Estimation, Dynamic WOLS,
Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)DelayedArray-0.22.0 A unified framework for working transparently with on-disk and in-memory array-like datasetsDelayedMatrixStats-1.18.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ ObjectsDeriv-4.1.3 Symbolic DifferentiationDescTools-0.99.44 Tools for Descriptive StatisticsDiagrammeR-1.0.9 Graph/Network VisualizationDiceDesign-1.9 Designs of Computer ExperimentsDiceKriging-1.6.0 Kriging Methods for Computer ExperimentsDiffBind-3.6.0 Differential Binding Analysis of ChIP-Seq Peak DataDirichletMultinomial-1.38.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataDiscriMiner-0.1-29 Tools of the Trade for Discriminant AnalysisDistributionUtils-0.6-0 Distribution UtilitiesDynDoc-1.74.0 Dynamic document toolsEBImage-4.38.0 Image processing and analysis toolbox for RECOSolveR-0.5.4 Embedded Conic Solver in RENMeval-2.0.3 Automated Tuning and Evaluations of Ecological Niche ModelsEasyABC-1.5 Efficient Approximate Bayesian Computation Sampling SchemesEnvStats-2.7.0 Package for Environmental Statistics, Including US EPA GuidanceEpiModel-2.2.1 Mathematical Modeling of Infectious Disease DynamicsExact-3.1 Unconditional Exact TestExperimentHub-2.4.0 Client to access ExperimentHub resourcesFDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probesFME-1.3.6.2 A Flexible Modelling Environment for Inverse Modelling,
Sensitivity, Identifiability and Monte Carlo AnalysisFNN-1.1.3 Fast Nearest Neighbor Search Algorithms and ApplicationsFactoMineR-2.4 Multivariate Exploratory Data Analysis and Data MiningFactorCopula-0.8 Factor, Bi-Factor and Second-Order Copula ModelsFlowSOM-2.4.0 Using self-organizing maps for visualization and interpretation of cytometry dataFormula-1.2-4 Extended Model FormulasGENESIS-2.26.0 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessGEOquery-2.64.0 Get data from NCBI Gene Expression Omnibus (GEO)GGally-2.1.2 Extension to ‘ggplot2’GJRM-0.2-6 Generalised Joint Regression ModellingGO.db-3.15.0 A set of annotation maps describing the entire Gene OntologyGOSemSim-2.22.0 GO-terms Semantic Similarity MeasuresGOstats-2.62.0 Tools for manipulating GO and microarraysGPArotation-2022.4-1 GPA Factor RotationGPfit-1.0-8 Gaussian Processes ModelingGSA-1.03.2 Gene Set AnalysisGSEABase-1.58.0 Gene set enrichment data structures and methodsGSVA-1.44.0 Gene Set Variation Analysis for microarray and RNA-seq dataGUTS-1.2.3 Fast Calculation of the Likelihood of a Stochastic Survival
ModelGWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association StudiesGWASTools-1.42.0 Tools for Genome Wide Association StudiesGenSA-1.1.7 Generalized Simulated AnnealingGeneNet-1.2.16 Modeling and Inferring Gene NetworksGenomeGraphs 1.46.0
GenomeInfoDb-1.32.1 Utilities for manipulating chromosome names, including modifying them to follow a particular naming styleGenomeInfoDbData-1.2.8 Species and taxonomy ID look up tables used by GenomeInfoDbGenomicAlignments-1.32.0 Representation and manipulation of short genomic alignmentsGenomicFeatures-1.48.0 Conveniently import and query gene modelsGenomicFiles-1.32.0 Distributed computing by file or by rangeGenomicRanges-1.48.0 Representation and manipulation of genomic intervalsGetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable InterpolationGillespieSSA-0.6.2 Gillespie’s Stochastic Simulation Algorithm (SSA)Glimma-2.6.0 Interactive HTML graphicsGlobalOptions-0.1.2 Generate Functions to Get or Set Global OptionsGmisc-3.0.0 Descriptive Statistics, Transition Plots, and MoreGreyListChIP-1.28.0 Grey Lists – Mask Artefact Regions Based on ChIP InputsGviz-1.40.0 Plotting data and annotation information along genomic coordinatesGxEScanR-2.0.2 Run GWAS/GWEIS Scans Using Binary Dosage FilesHDF5Array-1.24.0 HDF5 backend for DelayedArray objectsHMMcopy-1.38.0 Copy number prediction with correction for GC and mappability bias for HTS dataHSMMSingleCell-1.16.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)HWxtest-1.1.9 Exact Tests for Hardy-Weinberg ProportionsHaploSim-1.8.4 Functions to simulate haplotypesHiddenMarkov-1.8-13 Hidden Markov ModelsHmisc-4.7-0 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-1.24.0 Independent Hypothesis WeightingIRanges-2.30.0 Foundation of integer range manipulation in BioconductorIRdisplay-1.1 ‘Jupyter’ Display MachineryISOcodes-2022.01.10 Selected ISO CodesIlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arraysInteractionSet-1.24.0 Base Classes for Storing Genomic Interaction DataIso-0.0-18.1 Functions to Perform Isotonic RegressionJADE-2.0-3 Blind Source Separation Methods Based on Joint Diagonalization
and Some BSS Performance CriteriaJBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J.
ButtlarKEGGREST-1.36.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)KEGGgraph-1.56.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorKODAMA-1.9 Knowledge Discovery by Accuracy MaximizationKernSmooth-2.23-20 Functions for Kernel Smoothing Supporting Wand & Jones (1995)LaplacesDemon-16.1.6 Complete Environment for Bayesian InferenceLearnBayes-2.15.1 Functions for Learning Bayesian InferenceLmoments-1.3-1 L-Moments and Quantile MixturesLogicReg-1.6.4 Logic RegressionLymphoSeq-1.24.0 Analyze high-throughput sequencing of T and B cell receptorsLymphoSeqDB-0.99.2 LymphoSeq annotation databasesMAGeCKFlute-2.0.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic ScreensMALDIquant-1.21 Quantitative Analysis of Mass Spectrometry DataMASS-7.3-57 Support Functions and Datasets for Venables and Ripley’s MASSMAST-1.22.0 Model-based Analysis of Single Cell TranscriptomicsMCMCglmm-2.33 MCMC Generalised Linear Mixed ModelsMCMCpack-1.6-3 Markov Chain Monte Carlo (MCMC) PackageMIIVsem-0.5.8 Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation ModelsMPV-1.57 Data Sets from Montgomery, Peck and ViningMatchIt-4.3.4 Nonparametric Preprocessing for Parametric Causal InferenceMatching-4.10-2 Multivariate and Propensity Score Matching with Balance
OptimizationMatrix-1.4-1 Sparse and Dense Matrix Classes and MethodsMatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
OperationsMatrixExtra-0.1.9-1 Extra Methods for Sparse MatricesMatrixGenerics-1.8.0 S4 Generic Summary Statistic Functions that Operate on Matrix-Like ObjectsMatrixModels-0.5-0 Modelling with Sparse and Dense MatricesMfuzz-2.56.0 Soft clustering of time series gene expression dataModelMetrics-1.2.2.2 Rapid Calculation of Model MetricsNADA-1.6-1.1 Nondetects and Data Analysis for Environmental DataNCmisc-1.1.6 Miscellaneous Functions for Creating Adaptive Functions and
ScriptsNISTunits-1.0.1 Fundamental Physical Constants and Unit Conversions from NISTNLP-0.2-1 Natural Language Processing InfrastructureNOISeq-2.40.0 Exploratory analysis and differential expression for RNA-seq dataOceanView-1.0.6 Visualisation of Oceanographic Data and Model OutputOpenMx-2.20.6 Extended Structural Equation ModellingOrganismDbi-1.38.0 Software to enable the smooth interfacing of different database packagesPBSddesolve-1.12.6 Solver for Delay Differential EquationsPCAmatchR-0.3.2 Match Cases to Controls Based on Genotype Principal ComponentsPFAM.db-3.15.0 A set of protein ID mappings for PFAMPICS-2.40.0 Probabilistic inference of ChIP-seqParamHelpers-1.14 Helpers for Parameters in Black-Box Optimization, Tuning and
Machine LearningPearsonDS-1.2.2 Pearson Distribution SystemPermAlgo-1.1 Permutational Algorithm to Simulate Survival DataPoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log
linear modelPolynomF-2.0-3 Polynomials in RPresenceAbsence-1.1.10 Presence-Absence Model EvaluationProtGenerics-1.28.0 Generic infrastructure for Bioconductor mass spectrometry packagesQUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix EstimationR.cache-0.15.0 Fast and Light-Weight Caching (Memoization) of Objects and
Results to Speed Up ComputationsR.matlab-3.6.2 Read and Write MAT Files and Call MATLAB from Within RR.methodsS3-1.8.1 S3 Methods SimplifiedR.oo-1.24.0 R Object-Oriented Programming with or without ReferencesR.rsp-0.44.0 Dynamic Generation of Scientific ReportsR.utils-2.11.0 Various Programming UtilitiesR2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’R2jags-0.7-1 Using R to Run ‘JAGS’R6-2.5.1 Encapsulated Classes with Reference SemanticsRANN-2.6.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
MetricRBGL-1.72.0 An interface to the BOOST graph libraryRCAL-2.0 Regularized Calibrated EstimationRCircos-1.2.2 Circos 2D Track PlotRColorBrewer-1.1-3 ColorBrewer PalettesRCurl-1.98-1.6 General Network (HTTP/FTP/…) Client Interface for RREDCapR-1.0.0 Interaction Between R and REDCapRGCCA-2.1.2 Regularized and Sparse Generalized Canonical Correlation
Analysis for Multiblock DataRInside-0.2.17 C++ Classes to Embed R in C++ (and C) ApplicationsRItools-0.1-18 Randomization Inference ToolsRJSONIO-1.3-1.6 Serialize R Objects to JSON, JavaScript Object NotationRLRsim-3.1-8 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
ModelsRMTstat-0.3.1 Distributions, Statistics and Tests Derived from Random Matrix
TheoryRNASeqPower-1.36.0 Sample size for RNAseq studiesRNeXML-2.4.6 Semantically Rich I/O for the ‘NeXML’ FormatRNifti-1.4.0 Fast R and C++ Access to NIfTI ImagesROCR-1.0-11 Visualizing the Performance of Scoring ClassifiersROI-1.0-0 R Optimization InfrastructureROI.plugin.glpk-1.0-0 ‘ROI’ Plug-in ‘GLPK’RPMM-1.25 Recursively Partitioned Mixture ModelRPostgreSQL-0.7-3 R Interface to the ‘PostgreSQL’ Database SystemRPresto-1.3.7 DBI Connector to PrestoRProtoBufLib-2.8.0 C++ headers and static libraries of Protocol buffersRSNNS-0.4-14 Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)RSQLite-2.2.12 SQLite Interface for RRSclient-0.7-8 Client for RserveRSpectra-0.16-1 Solvers for Large-Scale Eigenvalue and SVD ProblemsRUnit-0.4.32 R Unit Test FrameworkRWeka-0.4-44 R/Weka InterfaceRWekajars-3.9.3-2 R/Weka Interface JarsRborist-0.2-3 Extensible, Parallelizable Implementation of the Random Forest
AlgorithmRcgmin-2013-2.21 Conjugate Gradient Minimization of Nonlinear Functions with Box
ConstraintsRcpp-1.0.8.3 Seamless R and C++ IntegrationRcppAnnoy-0.0.19 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
NeighborsRcppArmadillo-0.11.0.0.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra
LibraryRcppCCTZ-0.2.10 ‘Rcpp’ Bindings for the ‘CCTZ’ LibraryRcppDate-0.0.3 ‘date’ C++ Header Library for Date and Time FunctionalityRcppEigen-0.3.3.9.2 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra
LibraryRcppGSL-0.3.11 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and MatricesRcppHNSW-0.3.0 ‘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 LibrariesRcppParallel-5.1.5 Parallel Programming Tools for ‘Rcpp’RcppProgress-0.4.2 An Interruptible Progress Bar with OpenMP Support for C++ in R
PackagesRcppRoll-0.3.0 Efficient Rolling / Windowed OperationsRcppTOML-0.1.7 ‘Rcpp’ Bindings to Parser for Tom’s Obvious Markup LanguageRcppThread-2.1.3 R-Friendly Threading in C++RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG
ImplementationsRdpack-2.3 Update and Manipulate Rd Documentation ObjectsRdsdp-1.0.5.1 R Interface to DSDP Semidefinite Programming LibraryRefFreeEWAS-2.2 EWAS using Reference-Free DNA Methylation Mixture DeconvolutionReportingTools-2.36.0 Tools for making reports in various formatsRfast-2.0.6 A Collection of Efficient and Extremely Fast R FunctionsRglpk-0.6-4 R/GNU Linear Programming Kit InterfaceRgraphviz-2.40.0 Provides plotting capabilities for R graph objectsRhdf5lib-1.18.0 hdf5 library as an R packageRhpc-0.21-247 Permits *apply() Style Dispatch for ‘HPC’RhpcBLASctl-0.21-247.1 Control the Number of Threads on ‘BLAS’Rhtslib-1.28.0 HTSlib high-throughput sequencing library as an R packageRingo-1.60.0 R Investigation of ChIP-chip OligoarraysRlabkey-2.8.4 Data Exchange Between R and ‘LabKey’ ServerRmpfr-0.8-7 R MPFR - Multiple Precision Floating-Point ReliableRmpi-0.6-9.2 Interface (Wrapper) to MPI (Message-Passing Interface)Rook-1.1-1 Rook - a web server interface for RRsamtools-2.12.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importRserve-1.8-10 Binary R serverRsolnp-1.16 General Non-Linear OptimizationRssa-1.0.4 A Collection of Methods for Singular Spectrum AnalysisRsubread-2.10.0 Mapping, quantification and variant analysis of sequencing dataRtsne-0.16 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
ImplementationRttf2pt1-1.3.10 ‘ttf2pt1’ ProgramRvmmin-2018-4.17.1 Variable Metric Nonlinear Function MinimizationS4Vectors-0.34.0 Foundation of vector-like and list-like containers in BioconductorSBdecomp-1.2 Estimation of the Proportion of SB Explained by ConfoundersSDMTools-1.1-221.2 Species Distribution Modelling Tools: Tools for processing data
associated with species distribution modelling exercisesSKAT-2.2.4 SNP-Set (Sequence) Kernel Association TestSNPRelate-1.30.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)SNPassoc-2.0-11 SNPs-Based Whole Genome Association StudiesSOAR-0.99-11 Memory management in R by delayed assignmentsSPAtest-3.1.2 Score Test and Meta-Analysis Based on Saddlepoint ApproximationSPIA-2.48.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsSQUAREM-2021.1 Squared Extrapolation Methods for Accelerating EM-Like Monotone
AlgorithmsScaledMatrix-1.4.0 Creating a DelayedMatrix of Scaled and Centered ValuesSemiPar-1.0-4.2 Semiparametic RegressionSeqArray-1.36.0 Data management of large-scale whole-genome sequence variant callsSeqVarTools-1.34.0 Tools for variant dataShortRead-1.54.0 FASTQ input and manipulationSignifReg-4.3 Consistent Significance Controlled Variable Selection in
Generalized Linear RegressionSimSeq-1.4.0 Nonparametric Simulation of RNA-Seq DataSingleCellExperiment-1.18.0 S4 Classes for Single Cell DataSnowballC-0.7.0 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 LibrarySparseM-1.81 Sparse Linear AlgebraStanHeaders-2.21.0-7 C++ Header Files for StanStatMatch-1.4.1 Statistical Matching or Data FusionSummarizedExperiment-1.26.0 SummarizedExperiment containerSuperLearner-2.0-28 Super Learner PredictionSuppDists-1.1-9.7 Supplementary DistributionsTFBSTools-1.34.0 Software Package for Transcription Factor Binding Site (TFBS) AnalysisTFMPvalue-0.0.8 Efficient and Accurate P-Value Computation for Position Weight
MatricesTFisher-0.2.0 Optimal Thresholding Fisher’s P-Value Combination MethodTH.data-1.1-0 TH’s Data ArchiveTMB-1.8.1 Template Model Builder: A General Random Effect Tool Inspired by
‘ADMB’TTR-0.24.3 Technical Trading RulesTeachingDemos-2.12 Demonstrations for Teaching and LearningTitanCNA-1.34.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumoursTraMineR-2.2-3 Trajectory Miner: a Toolbox for Exploring and Rendering
SequencesTxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)UpSetR-1.4.0 A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting SetsV8-4.1.0 Embedded JavaScript and WebAssembly Engine for RVGAM-1.1-6 Vector Generalized Linear and Additive ModelsVIM-6.1.1 Visualization and Imputation of Missing ValuesVSURF-1.1.0 Variable Selection Using Random ForestsVariantAnnotation-1.42.0 Annotation of Genetic VariantsVennDiagram-1.7.3 Generate High-Resolution Venn and Euler PlotsVineCopula-2.4.3 Statistical Inference of Vine CopulasWeightSVM-1.7-9 Subject Weighted Support Vector MachinesWikidataQueryServiceR-1.0.0 API Client Library for ‘Wikidata Query Service’WikidataR-2.3.3 Read-Write API Client Library for WikidataWikipediR-1.5.0 A MediaWiki API WrapperWrench-1.14.0 Wrench normalization for sparse count dataWriteXLS-6.4.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) FilesXML-3.99-0.9 Tools for Parsing and Generating XML Within R and S-PlusXVector-0.36.0 Foundation of external vector representation and manipulation in Bioconductorabc-2.1 Tools for Approximate Bayesian Computation (ABC)abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)abe-3.0.1 Augmented Backward Eliminationabind-1.4-5 Combine Multidimensional Arraysacepack-1.4.1 ACE and AVAS for Selecting Multiple Regression Transformationsadabag-4.2 Applies Multiclass AdaBoost.M1, SAMME and Baggingade4-1.7-19 Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciencesadmisc-0.26 Adrian Dusa’s Miscellaneousaffxparser-1.68.0 Affymetrix File Parsing SDKaffy-1.74.0 Methods for Affymetrix Oligonucleotide Arraysaffycoretools-1.68.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChipsaffyio-1.66.0 Tools for parsing Affymetrix data filesaggregation-1.0.1 p-Value Aggregation Methodsakima-0.6-3.3 Interpolation of Irregularly and Regularly Spaced Dataalabama-2022.4-1 Constrained Nonlinear Optimizationalr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Editionamap-0.8-18 Another Multidimensional Analysis Packageanimation-2.7 A Gallery of Animations in Statistics and Utilities to Create
Animationsannaffy-1.68.0 Annotation tools for Affymetrix biological metadataannotate-1.74.0 Annotation for microarraysaod-1.3.2 Analysis of Overdispersed Dataape-5.6-2 Analyses of Phylogenetics and Evolutionapeglm-1.18.0 Approximate posterior estimation for GLM coefficientsaplot-0.1.3 Decorate a ‘ggplot’ with Associated Informationargparse-2.1.5 Command Line Optional and Positional Argument Parserargparser-0.7.1 Command-Line Argument Parserarm-1.12-2 Data Analysis Using Regression and Multilevel/Hierarchical
Modelsarsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical
Summariesarules-1.7-3 Mining Association Rules and Frequent Itemsetsash-1.0-15 David Scott’s ASH Routinesashr-2.2-54 Methods for Adaptive Shrinkage, using Empirical Bayesaskpass-1.1 Safe Password Entry for R, Git, and SSHasnipe-1.1.16 Animal Social Network Inference and Permutations for Ecologistsassertive-0.3-6 Readable Check Functions to Ensure Code Integrityassertive.base-0.0-9 A Lightweight Core of the ‘assertive’ Packageassertive.code-0.0-3 Assertions to Check Properties of Codeassertive.data-0.0-3 Assertions to Check Properties of Dataassertive.data.uk-0.0-2 Assertions to Check Properties of Stringsassertive.data.us-0.0-2 Assertions to Check Properties of Stringsassertive.datetimes-0.0-3 Assertions to Check Properties of Dates and Timesassertive.files-0.0-2 Assertions to Check Properties of Filesassertive.matrices-0.0-2 Assertions to Check Properties of Matricesassertive.models-0.0-2 Assertions to Check Properties of Modelsassertive.numbers-0.0-2 Assertions to Check Properties of Numbersassertive.properties-0.0-5 Assertions to Check Properties of Variablesassertive.reflection-0.0-5 Assertions for Checking the State of Rassertive.sets-0.0-3 Assertions to Check Properties of Setsassertive.strings-0.0-3 Assertions to Check Properties of Stringsassertive.types-0.0-3 Assertions to Check Types of Variablesassertthat-0.2.1 Easy Pre and Post Assertionsaudio-0.1-10 Audio Interface for Raws-2.5-1 Adaptive Weights Smoothingaws.ec2metadata-0.2.0 Get EC2 Instance Metadataaws.s3-0.3.21 ‘AWS S3’ Client Packageaws.signature-0.6.0 Amazon Web Services Request SignaturesawsMethods-1.1-1 Class and Methods Definitions for Packages ‘aws’, ‘adimpro’,
‘fmri’, ‘dwi’babelgene-22.3 Gene Orthologs for Model Organisms in a Tidy Data Formatbackports-1.4.1 Reimplementations of Functions Introduced Since R-3.0.0bacr-1.0.1 Bayesian Adjustment for Confoundingbamsignals-1.28.0 Extract read count signals from bam filesbartMachine-1.2.6 Bayesian Additive Regression TreesbartMachineJARs-1.1 bartMachine JARsbase built in
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