Known Issues
None
Package List
ADGofTest-0.3 Anderson-Darling GoF testALDEx2-1.14.1 Analysis Of Differential Abundance Taking Sample Variation Into AccountASCAT 2.5.2
AUC-0.3.0 Threshold independent performance measures for probabilistic<U+000a>classifiers.AgiMicroRna-2.32.0 Processing and Differential Expression Analysis of Agilent microRNA chipsAlgDesign-1.1-7.3 Algorithmic Experimental DesignAnnotationDbi-1.44.0 Annotation Database InterfaceAnnotationFilter-1.6.0 Facilities for Filtering Bioconductor Annotation ResourcesAnnotationForge-1.24.0 Code for Building Annotation Database PackagesAnnotationHub-2.14.4 Client to access AnnotationHub resourcesBB-2014.10-1 Solving and Optimizing Large-Scale Nonlinear SystemsBBmisc-1.11 Miscellaneous Helper Functions for B. BischlBDgraph-2.55 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMCBH-1.69.0-1 Boost C++ Header FilesBSgenome-1.50.0 Software infrastructure for efficient representation of full genomes and their SNPsBSgenome.Hsapiens.UCSC.hg19-1.4.0 Full genome sequences for Homo sapiens (UCSC version hg19)BatchJobs-1.7 Batch Computing with RBayesianTools-0.1.6 General-Purpose MCMC and SMC Samplers and Tools for Bayesian
StatisticsBhat-0.9-10 General likelihood explorationBiasedUrn-1.07 Biased Urn Model DistributionsBiobase-2.42.0 Biobase: Base functions for BioconductorBiocGenerics-0.28.0 S4 generic functions for BioconductorBiocInstaller-1.32.1 Install/Update Bioconductor, CRAN, and github PackagesBiocManager-1.30.4 Access the Bioconductor Project Package RepositoryBiocParallel-1.16.6 Bioconductor facilities for parallel evaluationBiostrings-2.50.2 Efficient manipulation of biological stringsBivarP-1.0 Estimating the Parameters of Some Bivariate DistributionsBolstad-0.2-40 Functions for Elementary Bayesian InferenceBolstad2-1.0-28 Bolstad functionsBradleyTerry2-1.0-9 Bradley-Terry ModelsBrobdingnag-1.2-6 Very Large Numbers in RCGEN-3.18.0 An R package for analysis of case-control studies in genetic epidemiologyCGHbase-1.42.0 CGHbase: Base functions and classes for arrayCGH data analysis.CVST-0.2-2 Fast Cross-Validation via Sequential TestingCairo-1.5-9 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-2.48.1 Category AnalysisComICS-1.0.4 Computational Methods for Immune Cell-Type SubsetsCompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal VariablesDAAG-1.22.1 Data Analysis and Graphics Data and FunctionsDBI-1.0.0 R Database InterfaceDEGseq-1.36.1 Identify Differentially Expressed Genes from RNA-seq dataDESeq-1.34.1 Differential gene expression analysis based on the negative binomial distributionDESeq2-1.22.2 Differential gene expression analysis based on the negative binomial distributionDEoptimR-1.0-8 Differential Evolution Optimization in Pure RDHARMa-0.2.4 Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression ModelsDNAcopy-1.56.0 DNA copy number data analysisDRR-0.0.3 Dimensionality Reduction via RegressionDT-0.5 A Wrapper of the JavaScript Library ‘DataTables’DTRreg-1.3 DTR Estimation and Inference via G-Estimation, Dynamic WOLS, and
Q-LearningDelayedArray-0.8.0 Delayed operations on array-like objectsDelayedMatrixStats-1.4.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ ObjectsDeriv-3.8.5 Symbolic DifferentiationDiagrammeR-1.0.0 Graph/Network VisualizationDiffBind-2.10.0 Differential Binding Analysis of ChIP-Seq Peak DataDiscriMiner-0.1-29 Tools of the Trade for Discriminant AnalysisDistributionUtils-0.6-0 Distribution UtilitiesDynDoc-1.60.0 Dynamic document toolsEBImage-4.24.0 Image processing and analysis toolbox for REasyABC-1.5 Efficient Approximate Bayesian Computation Sampling SchemesEpiModel-1.7.2 Mathematical Modeling of Infectious Disease DynamicsFDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probesFME-1.3.5 A Flexible Modelling Environment for Inverse Modelling,
Sensitivity, Identifiability and Monte Carlo AnalysisFNN-1.1.3 Fast Nearest Neighbor Search Algorithms and ApplicationsFactoMineR-1.41 Multivariate Exploratory Data Analysis and Data MiningFormula-1.2-3 Extended Model FormulasGENESIS-2.12.4 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessGEOquery-2.50.5 Get data from NCBI Gene Expression Omnibus (GEO)GGally-1.4.0 Extension to ‘ggplot2’GO.db-3.7.0 A set of annotation maps describing the entire Gene OntologyGOstats-2.48.0 Tools for manipulating GO and microarraysGSA-1.03.1 Gene Set AnalysisGSEABase-1.44.0 Gene set enrichment data structures and methodsGWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association StudiesGWASTools-1.28.0 Tools for Genome Wide Association StudiesGeneNet-1.2.13 Modeling and Inferring Gene NetworksGenomeGraphs-1.42.0 Plotting genomic information from EnsemblGenomeInfoDb-1.18.2 Utilities for manipulating chromosome and other ‘seqname’ identifiersGenomeInfoDbData-1.2.0 Species and taxonomy ID look up tables used by GenomeInfoDbGenomicAlignments-1.18.1 Representation and manipulation of short genomic alignmentsGenomicFeatures-1.34.4 Tools for making and manipulating transcript centric annotationsGenomicFiles-1.18.0 Distributed computing by file or by rangeGenomicRanges-1.34.0 Representation and manipulation of genomic intervals and variables defined along a genomeGetoptLong-0.1.7 Parsing Command-Line Arguments and Variable InterpolationGillespieSSA-0.5-4 Gillespie’s Stochastic Simulation Algorithm (SSA)GlobalOptions-0.1.0 Generate Functions to Get or Set Global OptionsGviz-1.26.5 Plotting data and annotation information along genomic coordinatesHCsnip 1.16.0
HDF5Array-1.10.1 HDF5 backend for DelayedArray objectsHMMcopy-1.24.0 Copy number prediction with correction for GC and mappability bias for HTS dataHWxtest-1.1.7 Exact Tests for Hardy-Weinberg ProportionsHaploSim-1.8.4 Functions to simulate haplotypesHmisc-4.2-0 Harrell MiscellaneousHomo.sapiens-1.3.1 Annotation package for the Homo.sapiens objectIDPmisc-1.1.19 ‘Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)’IRanges-2.16.0 Infrastructure for manipulating intervals on sequencesIRdisplay-0.7.0 ‘Jupyter’ Display MachineryIlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arraysIso-0.0-17 Functions to Perform Isotonic RegressionJBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J.
ButtlarKEGG.db-3.2.3 A set of annotation maps for KEGGKEGGREST-1.22.0 Client-side REST access to KEGGKEGGgraph-1.42.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorKEGGprofile-1.24.0 An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathwayKODAMA-1.5 Knowledge Discovery by Accuracy MaximizationKernSmooth-2.23-15 Functions for Kernel Smoothing Supporting Wand & Jones (1995)LearnBayes-2.15.1 Functions for Learning Bayesian InferenceLmoments-1.2-3 L-Moments and Quantile MixturesLogicReg-1.5.10 Logic RegressionLymphoSeq-1.10.0 Analyze high-throughput sequencing of T and B cell receptorsLymphoSeqDB-0.99.2 LymphoSeq annotation databasesMASS-7.3-51.1 Support Functions and Datasets for Venables and Ripley’s MASSMCMCglmm-2.28 MCMC Generalised Linear Mixed ModelsMCMCpack-1.4-4 Markov Chain Monte Carlo (MCMC) PackageMPV-1.53 Data Sets from Montgomery, Peck and ViningMatchIt-3.0.2 Nonparametric Preprocessing for Parametric Causal InferenceMatching-4.9-5 Multivariate and Propensity Score Matching with Balance
OptimizationMatrix-1.2-16 Sparse and Dense Matrix Classes and MethodsMatrixModels-0.4-1 Modelling with Sparse And Dense MatricesMfuzz-2.42.0 Soft clustering of time series gene expression dataModelMetrics-1.2.2 Rapid Calculation of Model MetricsMotIV-1.38.0 Motif Identification and ValidationNLP-0.2-0 Natural Language Processing InfrastructureNMF-0.21.0 Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)NOISeq-2.26.1 Exploratory analysis and differential expression for RNA-seq dataOceanView-1.0.4 Visualisation of Oceanographic Data and Model OutputOrganismDbi-1.24.0 Software to enable the smooth interfacing of different database packagesPBSddesolve-1.12.4 Solver for Delay Differential EquationsPFAM.db-3.7.0 A set of protein ID mappings for PFAMPICS-2.26.0 Probabilistic inference of ChIP-seqPKI-0.1-5.1 Public Key Infrastucture for R Based on the X.509 StandardParamHelpers-1.12 Helpers for Parameters in Black-Box Optimization, Tuning and
Machine LearningPoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log
linear modelPolynomF-1.0-2 Polynomials in RProtGenerics-1.14.0 S4 generic functions for Bioconductor proteomics infrastructureR.cache-0.13.0 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.methodsS3-1.7.1 S3 Methods SimplifiedR.oo-1.22.0 R Object-Oriented Programming with or without ReferencesR.rsp-0.43.1 Dynamic Generation of Scientific ReportsR.utils-2.8.0 Various Programming UtilitiesR2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’R2jags-0.5-7 Using R to Run ‘JAGS’R6-2.4.0 Encapsulated Classes with Reference SemanticsRANN-2.6.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
MetricRBGL-1.58.1 An interface to the BOOST graph libraryRCircos-1.2.0 Circos 2D Track PlotRColorBrewer-1.1-2 ColorBrewer PalettesRCurl-1.95-4.12 General Network (HTTP/FTP/…) Client Interface for RREDCapR-0.9.8 Interaction Between R and REDCapRGCCA-2.1.2 Regularized and Sparse Generalized Canonical Correlation
Analysis for Multiblock DataRInside-0.2.15 C++ Classes to Embed R in C++ ApplicationsRItools-0.1-16 Randomization Inference ToolsRJSONIO-1.3-1.1 Serialize R Objects to JSON, JavaScript Object NotationRLRsim-3.1-3 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
ModelsRMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix<U+000a>TheoryRMySQL-0.10.17 Database Interface and ‘MySQL’ Driver for RRNASeqPower-1.22.1 Sample size for RNAseq studiesRNeXML-2.3.0 Semantically Rich I/O for the ‘NeXML’ FormatROCR-1.0-7 Visualizing the Performance of Scoring ClassifiersRPostgreSQL-0.6-2 R Interface to the ‘PostgreSQL’ Database SystemRProtoBufLib-1.4.0 C++ headers and static libraries of Protocol buffersRSNNS-0.4-11 Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)RSQLite-2.1.1 ‘SQLite’ Interface for RRSclient-0.7-3 Client for RserveRSpectra-0.13-1 Solvers for Large-Scale Eigenvalue and SVD ProblemsRUnit-0.4.32 R Unit Test FrameworkRWeka-0.4-40 R/Weka InterfaceRWekajars-3.9.3-1 R/Weka Interface JarsRcpp-1.0.0 Seamless R and C++ IntegrationRcppArmadillo-0.9.200.7.1 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra
LibraryRcppEigen-0.3.3.5.0 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra
LibraryRcppGSL-0.3.6 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and MatricesRcppParallel-4.4.2 Parallel Programming Tools for ‘Rcpp’RcppProgress-0.4.1 An Interruptible Progress Bar with OpenMP Support for C++ in R
PackagesRcppRoll-0.3.0 Efficient Rolling / Windowed OperationsRdpack-0.10-1 Update and Manipulate Rd Documentation ObjectsReportingTools-2.22.1 Tools for making reports in various formatsRglpk-0.6-4 R/GNU Linear Programming Kit InterfaceRgraphviz-2.26.0 Provides plotting capabilities for R graph objectsRhdf5lib-1.4.2 hdf5 library as an R packageRhpc-0.18-204 Permits *apply() Style Dispatch for ‘HPC’Ringo-1.46.0 R Investigation of ChIP-chip OligoarraysRlabkey-2.2.4 Data Exchange Between R and ‘LabKey’ ServerRmpi-0.6-9 Interface (Wrapper) to MPI (Message-Passing Interface)Rook-1.1-1 Rook - a web server interface for RRsamtools-1.34.1 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importRssa-1.0 A Collection of Methods for Singular Spectrum AnalysisRsubread-1.32.4 Subread sequence alignment and counting for RRtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
ImplementationRttf2pt1-1.3.7 ‘ttf2pt1’ ProgramS4Vectors-0.20.1 S4 implementation of vector-like and list-like objectsSDMTools-1.1-221 Species Distribution Modelling Tools: Tools for processing data
associated with species distribution modelling exercisesSKAT-1.3.2.1 SNP-Set (Sequence) Kernel Association TestSNPRelate-1.16.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)SPIA-2.34.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsSQUAREM-2017.10-1 Squared Extrapolation Methods for Accelerating EM-Like Monotone
AlgorithmsSeqArray-1.22.6 Data Management of Large-scale Whole-genome Sequence Variant CallsSeqVarTools-1.20.2 Tools for variant dataShortRead-1.40.0 FASTQ input and manipulationSimSeq-1.4.0 Nonparametric Simulation of RNA-Seq DataSparseM-1.77 Sparse Linear AlgebraStanHeaders-2.18.1 C++ Header Files for StanSummarizedExperiment-1.12.0 SummarizedExperiment containerSuperLearner-2.0-24 Super Learner PredictionSuppDists-1.1-9.4 Supplementary DistributionsTH.data-1.0-10 TH’s Data ArchiveTMB-1.7.15 Template Model Builder: A General Random Effect Tool Inspired by
‘ADMB’TTR-0.23-4 Technical Trading RulesTeachingDemos-2.10 Demonstrations for Teaching and LearningTitanCNA-1.20.1 Subclonal copy number and LOH prediction from whole genome sequencing of tumoursTraMineR-2.0-10 Trajectory Miner: a Toolbox for Exploring and Rendering
SequencesTxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)UpSetR-1.3.3 A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting SetsVGAM-1.1-1 Vector Generalized Linear and Additive ModelsVIM-4.8.0 Visualization and Imputation of Missing ValuesVariantAnnotation-1.28.11 Annotation of Genetic VariantsVennDiagram-1.6.20 Generate High-Resolution Venn and Euler PlotsWikidataR-1.4.0 API Client Library for ‘Wikidata’WikipediR-1.5.0 A MediaWiki API WrapperWriteXLS-4.1.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) FilesXML-3.98-1.19 Tools for Parsing and Generating XML Within R and S-PlusXVector-0.22.0 Representation and manipulation of external sequencesabc-2.1 Tools for Approximate Bayesian Computation (ABC)abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)abind-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 Baggingade4-1.7-13 Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciencesadegenet-2.1.1 Exploratory Analysis of Genetic and Genomic Dataadephylo-1.1-11 Exploratory Analyses for the Phylogenetic Comparative Methodaffy-1.60.0 Methods for Affymetrix Oligonucleotide Arraysaffycoretools-1.54.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChipsaffyio-1.52.0 Tools for parsing Affymetrix data filesaggregation-1.0.1 p-Value Aggregation Methodsakima-0.6-2 Interpolation of Irregularly and Regularly Spaced Dataalr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Editionamap-0.8-16 Another Multidimensional Analysis Packageanimation-2.6 A Gallery of Animations in Statistics and Utilities to Create
Animationsannaffy-1.54.0 Annotation tools for Affymetrix biological metadataannotate-1.60.1 Annotation for microarraysaod-1.3.1 Analysis of Overdispersed Dataape-5.2 Analyses of Phylogenetics and Evolutionargparser-0.4 Command-Line Argument Parserarm-1.10-1 Data Analysis Using Regression and Multilevel/Hierarchical
Modelsaskpass-1.1 Safe Password Entry for R, Git, and SSHassertthat-0.2.0 Easy Pre and Post Assertionsaudio-0.1-5.1 Audio Interface for Raws.ec2metadata-0.1.5 Get EC2 Instance Metadataaws.s3-0.3.12 ‘AWS S3’ Client Packageaws.signature-0.4.4 Amazon Web Services Request Signaturesbackports-1.1.3 Reimplementations of Functions Introduced Since R-3.0.0base built in
base64-2.0 Base64 Encoder and Decoderbase64enc-0.1-3 Tools for base64 encodingbaySeq-2.16.0 Empirical Bayesian analysis of patterns of differential expression in count databayesm-3.1-1 Bayesian Inference for Marketing/Micro-Econometricsbdsmatrix-1.3-3 Routines for Block Diagonal Symmetric Matricesbeanplot-1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin<U+000a>Plot)beeswarm-0.2.3 The Bee Swarm Plot, an Alternative to Stripchartbenchmark-0.3-6 Benchmark Experiments Toolboxbibtex-0.4.2 Bibtex Parserbiglm-0.9-1 bounded memory linear and generalized linear modelsbigmemory-4.5.33 Manage Massive Matrices with Shared Memory and Memory-Mapped
Filesbigmemory.sri-0.1.3 A shared resource interface for Bigmemory Project packagesbindr-0.1.1 Parametrized Active Bindingsbindrcpp-0.2.2 An ‘Rcpp’ Interface to Active Bindingsbio3d-2.3-4 Biological Structure Analysisbiom-0.3.12 An interface package (beta) for the BIOM file format.biomaRt-2.38.0 Interface to BioMart databases (i.e. Ensembl)biovizBase-1.30.1 Basic graphic utilities for visualization of genomic data.bit-1.1-14 A Class for Vectors of 1-Bit Booleansbit64-0.9-7 A S3 Class for Vectors of 64bit Integersbitops-1.0-6 Bitwise Operationsblob-1.1.1 A Simple S3 Class for Representing Vectors of Binary Data
(‘BLOBS’)bmp-0.3 Read Windows Bitmap (BMP) Imagesbnlearn-4.4.1 Bayesian Network Structure Learning, Parameter Learning and
Inferencebold-0.8.6 Interface to Bold Systems APIboot-1.3-20 Bootstrap Functions (Originally by Angelo Canty for S)bootstrap-2017.2 Functions for the Book “An Introduction to the Bootstrap”breakaway-3.0 Species Richness Estimation and Modelingbrew-1.0-6 Templating Framework for Report Generationbrglm-0.6.1 Bias Reduction in Binomial-Response Generalized Linear Modelsbridgedist-0.1.0 An Implementation of the Bridge Distribution with Logit-Link as
in Wang and Louis (2003)bridgesampling-0.6-0 Bridge Sampling for Marginal Likelihoods and Bayes Factorsbroom-0.5.1 Convert Statistical Analysis Objects into Tidy Tibblesbst-0.3-17 Gradient Boostingbumphunter-1.24.5 Bump HuntercaTools-1.17.1.2 Tools: moving window statistics, GIF, Base64, ROC AUC, etc.calibrate-1.7.2 Calibration of Scatterplot and Biplot Axescallr-3.1.1 Call R from Rcar-3.0-2 Companion to Applied RegressioncarData-3.0-2 Companion to Applied Regression Data Setscaret-6.0-81 Classification and Regression Trainingcatdata-1.2.1 Categorical Datacellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columnscgdsr-1.2.10 R-Based API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS)cghFLasso-0.2-1 Detecting hot spot on CGH array data with fused lasso<U+000a>regression.checkmate-1.9.1 Fast and Versatile Argument Checkschemometrics-1.4.2 Multivariate Statistical Analysis in Chemometricschipseq-1.32.0 chipseq: A package for analyzing chipseq datachron-2.3-53 Chronological Objects which can Handle Dates and Timescirclize-0.4.5 Circular VisualizationclValid-0.6-6 Validation of Clustering Resultsclass-7.3-15 Functions for ClassificationclassInt-0.3-1 Choose Univariate Class Intervalscli-1.0.1 Helpers for Developing Command Line Interfacesclipr-0.5.0 Read and Write from the System Clipboardclisymbols-1.2.0 Unicode Symbols at the R Promptclue-0.3-57 Cluster Ensemblescluster-2.0.7-1 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et
al.clusterGeneration-1.3.4 Random Cluster Generation (with Specified Degree of Separation)clusterRepro-0.9 Reproducibility of Gene Expression Clustersclustree-0.3.0 Visualise Clusterings at Different Resolutionscoda-0.19-2 Output Analysis and Diagnostics for MCMCcodetools-0.2-16 Code Analysis Tools for Rcoin-1.3-0 Conditional Inference Procedures in a Permutation Test Frameworkcolorspace-1.4-0 A Toolbox for Manipulating and Assessing Colors and Palettescolourpicker-1.0 A Colour Picker Tool for Shiny and for Selecting Colours in
Plotscombinat-0.0-8 combinatorics utilitiescommonmark-1.7 High Performance CommonMark and Github Markdown Rendering in Rcompare-0.2-6 Comparing Objects for Differencescompositions-1.40-2 Compositional Data Analysisconfig-0.3 Manage Environment Specific Configuration Valuescopula-0.999-19 Multivariate Dependence with Copulascorpcor-1.6.9 Efficient Estimation of Covariance and (Partial) Correlationcowplot-0.9.4 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’coxme-2.2-10 Mixed Effects Cox Modelscrayon-1.3.4 Colored Terminal Outputcrosstalk-1.0.0 Inter-Widget Interactivity for HTML Widgetscrul-0.7.0 HTTP ClientcsSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarrayscubature-2.0.3 Adaptive Multivariate Integration over HypercubescummeRbund-2.24.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.curl-3.3 A Modern and Flexible Web Client for RcvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervalscytolib-1.4.1 C++ infrastructure for representing and interacting with the gated cytometryd3Network-0.5.2.1 Tools for creating D3 JavaScript network, tree, dendrogram, and<U+000a>Sankey graphs from Rdada2-1.10.1 Accurate, high-resolution sample inference from amplicon sequencing datadata.table-1.12.0 Extension of data.framedatasets built in
dbplyr-1.3.0 A ‘dplyr’ Back End for Databasesddalpha-1.3.8 Depth-Based Classification and Calculation of Data DepthdeSolve-1.21 Solvers for Initial Value Problems of Differential Equations
(‘ODE’, ‘DAE’, ‘DDE’)deal-1.2-39 Learning Bayesian Networks with Mixed Variablesdebugme-1.1.0 Debug R Packagesdegreenet-1.3-3 Models for Skewed Count Distributions Relevant to Networksdeldir-0.1-16 Delaunay Triangulation and Dirichlet (Voronoi) Tessellationdendextend-1.9.0 Extending ‘dendrogram’ Functionality in Rderfinder-1.16.1 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approachderfinderHelper-1.16.1 derfinder helper packagedesc-1.2.0 Manipulate DESCRIPTION Filesdescr-1.1.4 Descriptive Statisticsdevtools-2.0.1 Tools to Make Developing R Packages Easierdfoptim-2018.2-1 Derivative-Free Optimizationdiagram-1.6.4 Functions for Visualising Simple Graphs (Networks), Plotting
Flow Diagramsdiamonds-1.0-5 Analysis and sampling grids from diamond partitionsdichromat-2.0-0 Color Schemes for Dichromatsdigest-0.6.18 Create Compact Hash Digests of R ObjectsdimRed-0.2.2 A Framework for Dimensionality Reductiondiptest-0.75-7 Hartigan’s Dip Test Statistic for Unimodality - Correcteddismo-1.1-4 Species Distribution Modelingdistillery-1.0-4 Method Functions for Confidence Intervals and to Distill
Information from an Objectdistr-2.7.0 Object Oriented Implementation of DistributionsdistrEx-2.7.0 Extensions of Package ‘distr’diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis
PackagedoMC-1.3.5 Foreach Parallel Adaptor for ‘parallel’doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi PackagedoParallel-1.0.14 Foreach Parallel Adaptor for the ‘parallel’ PackagedoRNG-1.7.1 Generic Reproducible Parallel Backend for ‘foreach’ LoopsdoSNOW-1.0.16 Foreach Parallel Adaptor for the ‘snow’ PackagedotCall64-1.0-0 Enhanced Foreign Function Interface Supporting Long Vectorsdownloader-0.4 Download Files over HTTP and HTTPSdplyr-0.8.0.1 A Grammar of Data Manipulationdtangle-0.3.1 Cell Type Deconvolution from Gene Expressionsdtw-1.20-1 Dynamic Time Warping Algorithmsdummies-1.5.6 Create dummy/indicator variables flexibly and efficientlydynamicTreeCut-1.63-1 Methods for Detection of Clusters in Hierarchical Clustering
Dendrogramse1071-1.7-0.1 Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU WienedgeR-3.24.3 Empirical Analysis of Digital Gene Expression Data in Relasticnet-1.1.1 Elastic-Net for Sparse Estimation and Sparse PCAellipse-0.4.1 Functions for Drawing Ellipses and Ellipse-Like Confidence
Regionsellipsis-0.1.0 Tools for Working with …emulator-1.2-19 Bayesian Emulation of Computer Programsenergy-1.7-5 E-Statistics: Multivariate Inference via the Energy of Dataensembldb-2.6.7 Utilities to create and use Ensembl-based annotation databasesergm-3.9.4 Fit, Simulate and Diagnose Exponential-Family Models for
Networksergm.count-3.3.0 Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edgesevaluate-0.13 Parsing and Evaluation Tools that Provide More Details than the
Defaultexpm-0.999-3 Matrix Exponential, Log, ‘etc’expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”extRemes-2.0-9 Extreme Value Analysisextrafont-0.17 Tools for using fontsextrafontdb-1.0 Package for holding the database for the extrafont packagefail-1.3 File Abstraction Interface Layer (FAIL)fansi-0.4.0 ANSI Control Sequence Aware String Functionsfarver-1.1.0 Vectorised Colour Conversion and ComparisonfastICA-1.2-1 FastICA Algorithms to Perform ICA and Projection Pursuitfastcluster-1.1.25 Fast Hierarchical Clustering Routines for R and ‘Python’fastmatch-1.1-0 Fast match() functionfastseg-1.28.0 fastseg - a fast segmentation algorithmfasttime-1.0-2 Fast Utility Function for Time Parsing and Conversionfda-2.4.8 Functional Data Analysisfdrtool-1.2.15 Estimation of (Local) False Discovery Rates and Higher Criticismfeather-0.3.2 R Bindings to the Feather ‘API’ff-2.2-14 Memory-Efficient Storage of Large Data on Disk and Fast Access
Functionsffbase-0.12.7 Basic Statistical Functions for Package ‘ff’fftw-1.0-5 Fast FFT and DCT Based on the FFTW Libraryfftwtools-0.9-8 Wrapper for ‘FFTW3’ Includes: One-Dimensional Univariate,
One-Dimensional Multivariate, and Two-Dimensional Transformfields-9.6 Tools for Spatial Datafilehash-2.4-1 Simple Key-Value DatabasefishMod-0.29 Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta
Log-Normal Modelsfit.models-0.5-14 Compare Fitted Modelsfitdistrplus-1.0-14 Help to Fit of a Parametric Distribution to Non-Censored or
Censored DataflashClust-1.01-2 Implementation of optimal hierarchical clusteringflexclust-1.4-0 Flexible Cluster Algorithmsflexmix-2.3-15 Flexible Mixture ModelingflowClust-3.20.1 Clustering for Flow CytometryflowCore-1.48.1 flowCore: Basic structures for flow cytometry dataflowStats-3.40.1 Statistical methods for the analysis of flow cytometry dataflowViz-1.46.1 Visualization for flow cytometryflowWorkspace-3.30.2 Infrastructure for representing and interacting with gated and ungated cytometry data sets.fma-2.3 Data Sets from “Forecasting: Methods and Applications” by
Makridakis, Wheelwright & Hyndman (1998)forcats-0.4.0 Tools for Working with Categorical Variables (Factors)foreach-1.4.4 Provides Foreach Looping Construct for Rforecast-8.5 Forecasting Functions for Time Series and Linear Modelsforeign-0.8-71 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’,
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