Known Issues
Package List
- ALDEx2-1.32.0 Analysis Of Differential Abundance Taking Sample Variation Into Account
- ALL-1.42.0 A data package
- ASCAT 2.5.2 [CRAN]
- AgiMicroRna-2.50.0 Processing and Differential Expression Analysis of Agilent microRNA chips
- AnnotationDbi-1.62.1 Manipulation of SQLite-based annotations in Bioconductor
- AnnotationFilter-1.24.0 Facilities for Filtering Bioconductor Annotation Resources
- AnnotationForge-1.42.0 Tools for building SQLite-based annotation data packages
- AnnotationHub-3.8.0 Client to access AnnotationHub resources
- ArchR 1.0.1 [CRAN]
- BSgenome-1.68.0 Software infrastructure for efficient representation of full genomes and their SNPs
- BSgenome.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 Exploration
- Biobase-2.60.0 Biobase: Base functions for Bioconductor
- BiocFileCache-2.8.0 Manage Files Across Sessions
- BiocGenerics-0.46.0 S4 generic functions used in Bioconductor
- BiocIO-1.10.0 Standard Input and Output for Bioconductor Packages
- BiocManager-1.30.21 Access the Bioconductor Project Package Repository
- BiocNeighbors-1.18.0 Nearest Neighbor Detection for Bioconductor Packages
- BiocParallel-1.34.2 Bioconductor facilities for parallel evaluation
- BiocSingular-1.16.0 Singular Value Decomposition for Bioconductor Packages
- BiocStyle-2.28.0 Standard styles for vignettes and other Bioconductor documents
- BiocVersion-3.17.1 Set the appropriate version of Bioconductor packages
- Biostrings-2.68.1 Efficient manipulation of biological strings
- BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
- Bolstad-0.2-41 Functions for Elementary Bayesian Inference
- Bolstad2-1.0-29 Bolstad Functions
- BradleyTerry2-1.1-2 Bradley-Terry Models
- CATALYST-1.24.0 Cytometry dATa anALYSis Tools
- CGHbase-1.60.0 CGHbase: Base functions and classes for arrayCGH data analysis.
- CLONETv2-2.2.1 Clonality Estimates in Tumor
- CMA-1.58.0 Synthesis of microarray-based classification
- CNEr-1.36.0 CNE Detection and Visualization
- COMPASS-1.38.1 Combinatorial Polyfunctionality Analysis of Single Cells
- CVXR-1.0-11 Disciplined Convex Optimization
- Category-2.66.0 Category Analysis
- ChIPpeakAnno-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 ranges
- ChIPseeker-1.36.0 ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
- ComplexHeatmap-2.16.0 Make Complex Heatmaps
- ConsensusClusterPlus-1.64.0 ConsensusClusterPlus
- CytoML-2.12.0 A GatingML Interface for Cross Platform Cytometry Data Sharing
- DAAG-1.25.4 Data Analysis and Graphics Data and Functions
- DECIPHER-2.28.0 Tools for curating, analyzing, and manipulating biological sequences
- DEGseq-1.54.0 Identify Differentially Expressed Genes from RNA-seq data
- DESeq2-1.40.1 Differential gene expression analysis based on the negative binomial distribution
- DNAcopy-1.74.1 DNA copy number data analysis
- DO.db-2.9 A set of annotation maps describing the entire Disease Ontology
- DOSE-3.26.1 Disease Ontology Semantic and Enrichment analysis
- DOT-0.1 Render and Export DOT Graphs in R
- DelayedArray-0.26.3 A unified framework for working transparently with on-disk and in-memory array-like datasets
- DelayedMatrixStats-1.22.1 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
- DiceDesign-1.9 Designs of Computer Experiments
- DiffBind-3.10.0 Differential Binding Analysis of ChIP-Seq Peak Data
- DirichletMultinomial-1.42.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
- DynDoc-1.78.0 Dynamic document tools
- EBImage-4.42.0 Image processing and analysis toolbox for R
- ECOSolveR-0.5.5 Embedded Conic Solver in R
- EpiModel-2.3.2 Mathematical Modeling of Infectious Disease Dynamics
- ExperimentHub-2.8.0 Client to access ExperimentHub resources
- FDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probes
- FlowSOM-2.8.0 Using self-organizing maps for visualization and interpretation of cytometry data
- GENESIS-2.30.0 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
- GEOquery-2.68.0 Get data from NCBI Gene Expression Omnibus (GEO)
- GO.db-3.17.0 A set of annotation maps describing the entire Gene Ontology
- GOSemSim-2.26.0 GO-terms Semantic Similarity Measures
- GOstats-2.66.0 Tools for manipulating GO and microarrays
- GPfit-1.0-8 Gaussian Processes Modeling
- GSEABase-1.62.0 Gene set enrichment data structures and methods
- GSVA-1.48.1 Gene Set Variation Analysis for microarray and RNA-seq data
- GWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association Studies
- GWASTools-1.46.0 Tools for Genome Wide Association Studies
- GenomeInfoDb-1.36.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
- GenomeInfoDbData-1.2.10 Species and taxonomy ID look up tables used by GenomeInfoDb
- GenomicAlignments-1.36.0 Representation and manipulation of short genomic alignments
- GenomicFeatures-1.52.0 Conveniently import and query gene models
- GenomicFiles-1.36.0 Distributed computing by file or by range
- GenomicRanges-1.52.0 Representation and manipulation of genomic intervals
- Glimma-2.10.0 Interactive HTML graphics
- Gmisc-3.0.2 Descriptive Statistics, Transition Plots, and More
- GreyListChIP-1.32.0 Grey Lists – Mask Artefact Regions Based on ChIP Inputs
- Gviz-1.44.0 Plotting data and annotation information along genomic coordinates
- HDF5Array-1.28.1 HDF5 backend for DelayedArray objects
- HDO.db-0.99.1 A set of annotation maps describing the entire Human Disease Ontology
- HMMcopy-1.42.0 Copy number prediction with correction for GC and mappability bias for HTS data
- HSMMSingleCell-1.20.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)
- HaploSim-1.8.4.2 Functions to Simulate Haplotypes
- Homo.sapiens-1.3.1 Annotation package for the Homo.sapiens object
- IHW-1.28.0 Independent Hypothesis Weighting
- IRanges-2.34.0 Foundation of integer range manipulation in Bioconductor
- IRdisplay-1.1 ‘Jupyter’ Display Machinery
- IlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arrays
- InteractionSet-1.28.0 Base Classes for Storing Genomic Interaction Data
- KEGGREST-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 Bioconductor
- LogicReg-1.6.5 Logic Regression
- LymphoSeq-1.28.0 Analyze high-throughput sequencing of T and B cell receptors
- LymphoSeqDB-0.99.2 LymphoSeq annotation databases
- MAGeCKFlute-2.4.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
- MAST-1.26.0 Model-based Analysis of Single Cell Transcriptomics
- MCMCglmm-2.34 MCMC Generalised Linear Mixed Models
- MPV-1.62 Data Sets from Montgomery, Peck and Vining
- MatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
Operations
- MatrixExtra-0.1.13 Extra Methods for Sparse Matrices
- MatrixGenerics-1.12.2 S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
- Mfuzz-2.60.0 Soft clustering of time series gene expression data
- NADA-1.6-1.1 Nondetects and Data Analysis for Environmental Data
- NOISeq-2.44.0 Exploratory analysis and differential expression for RNA-seq data
- OrganismDbi-1.42.0 Software to enable the smooth interfacing of different database packages
- PBSddesolve-1.13.3 Solver for Delay Differential Equations
- PFAM.db-3.17.0 A set of protein ID mappings for PFAM
- PICS-2.44.0 Probabilistic inference of ChIP-seq
- PolynomF-2.0-5 Polynomials in R
- ProtGenerics-1.32.0 Generic infrastructure for Bioconductor mass spectrometry packages
- QUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix Estimation
- R2jags-0.7-1 Using R to Run ‘JAGS’
- RBGL-1.76.0 An interface to the BOOST graph library
- REDCapR-1.1.0 Interaction Between R and REDCap
- RLRsim-3.1-8 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
Models
- RNASeqPower-1.40.0 Sample size for RNAseq studies
- RPostgreSQL-0.7-5 R Interface to the ‘PostgreSQL’ Database System
- RPresto-1.4.5 DBI Connector to Presto
- RProtoBufLib-2.12.0 C++ headers and static libraries of Protocol buffers
- RSclient-0.7-9 Client for Rserve
- RVenn-1.1.0 Set Operations for Many Sets
- RcppAnnoy-0.0.20 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
Neighbors
- RcppCCTZ-0.2.12 ‘Rcpp’ Bindings for the ‘CCTZ’ Library
- RcppDate-0.0.3 ‘date’ C++ Header Library for Date and Time Functionality
- RcppHNSW-0.4.1 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest
Neighbors
- RcppML-0.3.7 Rcpp Machine Learning Library
- RcppNumerical-0.5-0 ‘Rcpp’ Integration for Numerical Computing Libraries
- RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG
Implementations
- Rdsdp-1.0.5.2.1 R Interface to DSDP Semidefinite Programming Library
- ReportingTools-2.39.0 Tools for making reports in various formats
- Rfast-2.0.7 A Collection of Efficient and Extremely Fast R Functions
- Rgraphviz-2.44.0 Provides plotting capabilities for R graph objects
- Rhdf5lib-1.22.0 hdf5 library as an R package
- Rhpc-0.21-247 Permits *apply() Style Dispatch for ‘HPC’
- Rhtslib-2.2.0 HTSlib high-throughput sequencing library as an R package
- Ringo-1.64.0 R Investigation of ChIP-chip Oligoarrays
- Rlabkey-2.11.0 Data Exchange Between R and ‘LabKey’ Server
- Rmpi-0.7-1 Interface (Wrapper) to MPI (Message-Passing Interface)
- Rsamtools-2.16.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
- Rsubread-2.14.2 Mapping, quantification and variant analysis of sequencing data
- S4Arrays-1.0.4 Foundation of array-like containers in Bioconductor
- S4Vectors-0.38.1 Foundation of vector-like and list-like containers in Bioconductor
- SNPRelate-1.34.1 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
- SNPassoc-2.1-0 SNPs-Based Whole Genome Association Studies
- SPIA-2.52.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
- ScaledMatrix-1.8.1 Creating a DelayedMatrix of Scaled and Centered Values
- SemiPar-1.0-4.2 Semiparametic Regression
- SeqArray-1.40.1 Data Management of Large-Scale Whole-Genome Sequence Variant Calls
- SeqVarTools-1.38.0 Tools for variant data
- ShortRead-1.58.0 FASTQ input and manipulation
- SingleCellExperiment-1.22.0 S4 Classes for Single Cell Data
- SummarizedExperiment-1.30.2 SummarizedExperiment container
- TFBSTools-1.38.0 Software Package for Transcription Factor Binding Site (TFBS) Analysis
- TFMPvalue-0.0.9 Efficient and Accurate P-Value Computation for Position Weight
Matrices
- TitanCNA-1.38.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
- TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)
- VariantAnnotation-1.46.0 Annotation of Genetic Variants
- Wrench-1.18.0 Wrench normalization for sparse count data
- XVector-0.40.0 Foundation of external vector representation and manipulation in Bioconductor
- affxparser-1.72.0 Affymetrix File Parsing SDK
- affy-1.78.0 Methods for Affymetrix Oligonucleotide Arrays
- affycoretools-1.72.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
- affyio-1.70.0 Tools for parsing Affymetrix data files
- alr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Edition
- amap-0.8-19 Another Multidimensional Analysis Package
- annaffy-1.72.0 Annotation tools for Affymetrix biological metadata
- annotate-1.78.0 Annotation for microarrays
- apeglm-1.22.1 Approximate posterior estimation for GLM coefficients
- argparser-0.7.1 Command-Line Argument Parser
- arsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical
Summaries
- arules-1.7-6 Mining Association Rules and Frequent Itemsets
- ash-1.0-15 David Scott’s ASH Routines
- ashr-2.2-54 Methods for Adaptive Shrinkage, using Empirical Bayes
- aws.ec2metadata-0.2.0 Get EC2 Instance Metadata
- aws.s3-0.3.21 ‘AWS S3’ Client Package
- aws.signature-0.6.0 Amazon Web Services Request Signatures
- babelgene-22.9 Gene Orthologs for Model Organisms in a Tidy Data Format
- bamsignals-1.32.0 Extract read count signals from bam files
- base64url-1.4 Fast and URL-Safe Base64 Encoder and Decoder
- basilisk-1.12.0 Freezing Python Dependencies Inside Bioconductor Packages
- basilisk.utils-1.12.1 Basilisk Installation Utilities
- batchtools-0.9.17 Tools for Computation on Batch Systems
- baySeq-2.31.0 Empirical Bayesian analysis of patterns of differential expression in count data
- beachmat-2.16.0 Compiling Bioconductor to Handle Each Matrix Type
- benchmark-0.3-6 Benchmark Experiments Toolbox
- bezier-1.1.2 Toolkit for Bezier Curves and Splines
- biglm-0.9-2.1 Bounded Memory Linear and Generalized Linear Models
- biomaRt-2.56.1 Interface to BioMart databases (i.e. Ensembl)
- biomformat-1.28.0 An interface package for the BIOM file format
- biovizBase-1.48.0 Basic graphic utilities for visualization of genomic data.
- bookdown-0.34 Authoring Books and Technical Documents with R Markdown
- breakaway-4.8.4 Species Richness Estimation and Modeling
- bumphunter-1.42.0 Bump Hunter
- catdata-1.2.3 Categorical Data
- chipseq-1.50.0 chipseq: A package for analyzing chipseq data
- chromVAR-1.22.1 Chromatin Variation Across Regions
- clusterProfiler-4.8.1 A universal enrichment tool for interpreting omics data
- colorRamps-2.3.1 Builds Color Tables
- compare-0.2-6 Comparing Objects for Differences
- config-0.3.1 Manage Environment Specific Configuration Values
- copynumber-1.38.0 Segmentation of single- and multi-track copy number data by penalized least squares regression.
- cummeRbund-2.42.0 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 Code
- cytolib-2.12.0 C++ infrastructure for representing and interacting with the gated cytometry data
- dada2-1.28.0 Accurate, high-resolution sample inference from amplicon sequencing data
- degreenet-1.3-3 Models for Skewed Count Distributions Relevant to Networks
- densvis-1.10.2 Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction
- depmap-1.14.0 Cancer Dependency Map Data Package
- derfinder-1.34.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
- derfinderHelper-1.34.0 derfinder helper package
- descr-1.1.7 Descriptive Statistics
- dfoptim-2020.10-1 Derivative-Free Optimization
- dials-1.2.0 Tools for Creating Tuning Parameter Values
- diamonds-1.0-5 Analysis and sampling grids from diamond partitions
- diffusionMap-1.2.0 Diffusion Map
- dir.expiry-1.8.0 Managing Expiration for Cache Directories
- doBy-4.6.16 Groupwise Statistics, LSmeans, Linear Estimates, Utilities
- doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
- dqrng-0.3.0 Fast Pseudo Random Number Generators
- drc-3.0-1 Analysis of Dose-Response Curves
- edgeR-3.42.4 Empirical Analysis of Digital Gene Expression Data in R
- egor-1.23.3 Import and Analyse Ego-Centered Network Data
- elasticnet-1.3 Elastic-Net for Sparse Estimation and Sparse PCA
- enrichplot-1.20.0 Visualization of Functional Enrichment Result
- ensembldb-2.24.0 Utilities to create and use Ensembl-based annotation databases
- epitools-0.5-10.1 Epidemiology Tools
- ergm.ego-1.1.0 Fit, Simulate and Diagnose Exponential-Family Random Graph
Models to Egocentrically Sampled Network Data
- etrunct-0.1 Computes Moments of Univariate Truncated t Distribution
- europepmc-0.4.1 R Interface to the Europe PubMed Central RESTful Web Service
- fANCOVA-0.6-1 Nonparametric Analysis of Covariance
- faraway-1.0.8 Functions and Datasets for Books by Julian Faraway
- fastseg-1.46.0 fastseg - a fast segmentation algorithm
- fasttime-1.1-0 Fast Utility Function for Time Parsing and Conversion
- fda-6.1.4 Functional Data Analysis
- fds-1.8 Functional Data Sets
- fgsea-1.26.0 Fast Gene Set Enrichment Analysis
- filelock-1.0.2 Portable File Locking
- fit.models-0.64 Compare Fitted Models
- float-0.3-1 32-Bit Floats
- flowClust-3.38.0 Clustering for Flow Cytometry
- flowCore-2.12.0 flowCore: Basic structures for flow cytometry data
- flowStats-4.12.0 Statistical methods for the analysis of flow cytometry data
- flowViz-1.64.0 Visualization for flow cytometry
- flowWorkspace-4.12.0 Infrastructure for representing and interacting with gated and ungated cytometry data sets.
- fontBitstreamVera-0.1.1 Fonts with ‘Bitstream Vera Fonts’ License
- fontLiberation-0.1.0 Liberation Fonts
- fontquiver-0.2.1 Set of Installed Fonts
- forestplot-3.1.1 Advanced Forest Plot Using ‘grid’ Graphics
- forge-0.2.0 Casting Values into Shape
- fts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)
- gage-2.50.0 Generally Applicable Gene-set Enrichment for Pathway Analysis
- gcrma-2.72.0 Background Adjustment Using Sequence Information
- gdsfmt-1.36.0
- gdtools-0.3.3 Utilities for Graphical Rendering and Fonts Management
- geneLenDataBase-1.36.0 Lengths of mRNA transcripts for a number of genomes
- genefilter-1.82.1 genefilter: methods for filtering genes from high-throughput experiments
- geneplotter-1.78.0 Graphics related functions for Bioconductor
- gfonts-0.2.0 Offline ‘Google’ Fonts for ‘Markdown’ and ‘Shiny’
- ggVennDiagram-1.2.2 A ‘ggplot2’ Implement of Venn Diagram
- ggbio-1.48.0 Visualization tools for genomic data
- ggcyto-1.28.0 Visualize Cytometry data with ggplot
- ggdendro-0.1.23 Create Dendrograms and Tree Diagrams Using ‘ggplot2’
- ggnewscale-0.4.9 Multiple Fill and Colour Scales in ‘ggplot2’
- ggpointdensity-0.1.0 A Cross Between a 2D Density Plot and a Scatter Plot
- ggrastr-1.0.2 Rasterize Layers for ‘ggplot2’
- ggthemes-4.2.4 Extra Themes, Scales and Geoms for ‘ggplot2’
- ggtree-3.8.0 an R package for visualization of tree and annotation data
- glmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox
Proportional Hazards Model
- goseq-1.52.0 Gene Ontology analyser for RNA-seq and other length biased data
- graph-1.78.0 graph: A package to handle graph data structures
- gson-0.1.0 Base Class and Methods for ‘gson’ Format
- gsubfn-0.7 Utilities for Strings and Function Arguments
- hapassoc-1.2-9 Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithm
- haplo.stats-1.9.3 Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
- hdrcde-3.4 Highest Density Regions and Conditional Density Estimation
- hgu133plus2.db-3.13.0 Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)
- hopach-2.60.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
- hypergate-0.8.3 Machine Learning of Hyperrectangular Gating Strategies for
High-Dimensional Cytometry
- igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
- illuminaio-0.42.0 Parsing Illumina Microarray Output Files
- impute-1.74.1 impute: Imputation for microarray data
- infer-1.0.4 Tidy Statistical Inference
- inferference-1.0.2 Methods for Causal Inference with Interference
- interactiveDisplayBase-1.38.0 Base package for enabling powerful shiny web displays of Bioconductor objects
- invgamma-1.1 The Inverse Gamma Distribution
- iotools-0.3-2 I/O Tools for Streaming
- its-1.1.8 Irregular Time Series
- karyoploteR-1.26.0 Plot customizable linear genomes displaying arbitrary data
- keyring-1.3.1 Access the System Credential Store from R
- kin.cohort-0.7 Analysis of Kin-Cohort Studies
- knockoff-0.3.6 The Knockoff Filter for Controlled Variable Selection
- kyotil-2023.2-2 Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studies
- latentnet-2.10.6 Latent Position and Cluster Models for Statistical Networks
- lgr-0.4.4 A Fully Featured Logging Framework
- limma-3.56.2 Linear Models for Microarray Data
- lintr-3.0.2 A ‘Linter’ for R Code
- lokern-1.1-10 Kernel Regression Smoothing with Local or Global Plug-in
Bandwidth
- lpridge-1.0-8 Local Polynomial (Ridge) Regression
- lpsymphony-1.28.1 Symphony integer linear programming solver in R
- lumi-2.52.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
- maSigPro-1.72.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
- mapdata-2.3.1 Extra Map Databases
- marray-1.78.0 Exploratory analysis for two-color spotted microarray data
- matrixStats-1.0.0 Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
- metagenomeSeq-1.42.0 Statistical analysis for sparse high-throughput sequencing
- methylKit-1.26.0 DNA methylation analysis from high-throughput bisulfite sequencing results
- methylumi-2.46.0 Handle Illumina methylation data
- minfi-1.46.0 Analyze Illumina Infinium DNA methylation arrays
- mixOmics-6.24.0 Omics Data Integration Project
- mixsqp-0.3-48 Sequential Quadratic Programming for Fast Maximum-Likelihood
Estimation of Mixture Proportions
- mlapi-0.1.1 Abstract Classes for Building ‘scikit-learn’ Like API
- modeldata-1.1.0 Data Sets Useful for Modeling Examples
- modelenv-0.1.1 Provide Tools to Register Models for Use in ‘tidymodels’
- mondate-0.10.02 Keep Track of Dates in Terms of Months
- motifmatchr-1.22.0 Fast Motif Matching in R
- msa-1.32.0 Multiple Sequence Alignment
- msigdbr-7.5.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
- multtest-2.56.0 Resampling-based multiple hypothesis testing
- nanotime-0.3.7 Nanosecond-Resolution Time Support for R
- ncdfFlow-2.46.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
- ndtv-0.13.3 Network Dynamic Temporal Visualizations
- networksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through
Sequential Importance Sampling
- numbers-0.8-5 Number-Theoretic Functions
- nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
- odbc-1.3.4 Connect to ODBC Compatible Databases (using the DBI Interface)
- oligo-1.64.1 Preprocessing tools for oligonucleotide arrays
- oligoClasses-1.62.0 Classes for high-throughput arrays supported by oligo and crlmm
- openCyto-2.12.0 Hierarchical Gating Pipeline for flow cytometry data
- org.Hs.eg.db-3.17.0 Genome wide annotation for Human
- org.Mm.eg.db-3.17.0 Genome wide annotation for Mouse
- osqp-0.6.0.8 Quadratic Programming Solver using the ‘OSQP’ Library
- pack-0.1-1 Convert values to/from raw vectors
- parsnip-1.1.0 A Common API to Modeling and Analysis Functions
- partools-1.1.6 Tools for the ‘Parallel’ Package
- pathview-1.40.0 a tool set for pathway based data integration and visualization
- pbs-1.1 Periodic B Splines
- pcaMethods-1.92.0 A collection of PCA methods
- pdftools-3.3.3 Text Extraction, Rendering and Converting of PDF Documents
- pdist-1.2.1 Partitioned Distance Function
- pedigree-1.4.2 Pedigree Functions
- pedigreemm-0.3-3 Pedigree-based mixed-effects models
- perm-1.0-0.2 Exact or Asymptotic Permutation Tests
- phyloseq-1.44.0 Handling and analysis of high-throughput microbiome census data
- poisbinom-1.0.1 A Faster Implementation of the Poisson-Binomial Distribution
- polyester-1.36.0 Simulate RNA-seq reads
- polyreg-0.8.0 Polynomial Regression
- poweRlaw-0.70.6 Analysis of Heavy Tailed Distributions
- premessa 0.2.6 [CRAN]
- preprocessCore-1.62.1 A collection of pre-processing functions
- psychotools-0.7-3 Psychometric Modeling Infrastructure
- qdapRegex-0.7.5 Regular Expression Removal, Extraction, and Replacement Tools
- qpdf-1.3.2 Split, Combine and Compress PDF Files
- qqconf-1.3.2 Creates Simultaneous Testing Bands for QQ-Plots
- qtl-1.60 Tools for Analyzing QTL Experiments
- quantoptr-0.1.3 Algorithms for Quantile- And Mean-Optimal Treatment Regimes
- quantsmooth-1.66.0 Quantile smoothing and genomic visualization of array data
- qvalue-2.32.0 Q-value estimation for false discovery rate control
- qvcalc-1.0.3 Quasi Variances for Factor Effects in Statistical Models
- r2d3-0.2.6 Interface to ‘D3’ Visualizations
- rARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD Problems
- rGADEM-2.48.0 de novo motif discovery
- rainbow-3.7 Bagplots, Boxplots and Rainbow Plots for Functional Data
- rbenchmark-1.0.0 Benchmarking routine for R
- refGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from
‘Ensembl’ and ‘UCSC’ Genome Browsers
- refund-0.1-30 Regression with Functional Data
- regioneR-1.32.0 Association analysis of genomic regions based on permutation tests
- regress-1.3-21 Gaussian Linear Models with Linear Covariance Structure
- regtools-1.7.0 Regression and Classification Tools
- relations-0.6-13 Data Structures and Algorithms for Relations
- relevent-1.2-1 Relational Event Models
- repr-1.1.6 Serializable Representations
- restfulr-0.0.15 R Interface to RESTful Web Services
- rgenoud-5.9-0.3 R Version of GENetic Optimization Using Derivatives
- rhandsontable-0.3.8 Interface to the ‘Handsontable.js’ Library
- rhdf5-2.44.0 R Interface to HDF5
- rhdf5filters-1.12.1 HDF5 Compression Filters
- rjags-4-14 Bayesian Graphical Models using MCMC
- rje-1.12.1 Miscellaneous Useful Functions for Statistics
- rsample-1.1.1 General Resampling Infrastructure
- rslurm-0.6.2 Submit R Calculations to a ‘Slurm’ Cluster
- rsparse-0.5.1 Statistical Learning on Sparse Matrices
- rstanarm-2.21.4 Bayesian Applied Regression Modeling via Stan
- rsvd-1.0.5 Randomized Singular Value Decomposition
- rtracklayer-1.60.0 R interface to genome annotation files and the UCSC genome browser
- rvcheck-0.2.1 R/Package Version Check
- rzmq-0.9.9 R Bindings for ‘ZeroMQ’
- samr-3.0 SAM: Significance Analysis of Microarrays
- scater-1.28.0 Single-Cell Analysis Toolkit for Gene Expression Data in R
- scattermore-1.2 Scatterplots with More Points
- schoolmath-0.4.1 Functions and Datasets for Math Used in School
- scidb-3.0.0 An R Interface to SciDB
- scrime-1.3.5 Analysis of High-Dimensional Categorical Data Such as SNP Data
- scs-3.2.4 Splitting Conic Solver
- scuttle-1.10.1 Single-Cell RNA-Seq Analysis Utilities
- seqLogo-1.66.0 Sequence logos for DNA sequence alignments
- seqminer-8.9 Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into R
- sequenza-3.0.0 Copy Number Estimation from Tumor Genome Sequencing Data
- sets-1.0-24 Sets, Generalized Sets, Customizable Sets and Intervals
- shinyBS-0.61.1 Twitter Bootstrap Components for Shiny
- shinyFiles-0.9.3 A Server-Side File System Viewer for Shiny
- shinycssloaders-1.0.0 Add Loading Animations to a ‘shiny’ Output While It’s
Recalculating
- siggenes-1.74.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
- sitmo-2.0.2 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header
Files
- slider-0.3.0 Sliding Window Functions
- snpStats-1.50.0 SnpMatrix and XSnpMatrix classes and methods
- sodium-1.2.1 A Modern and Easy-to-Use Crypto Library
- sparklyr-1.8.1 R Interface to Apache Spark
- sparseMatrixStats-1.12.0 Summary Statistics for Rows and Columns of Sparse Matrices
- sqldf-0.4-11 Manipulate R Data Frames Using SQL
- squash-1.0.9 Color-Based Plots for Multivariate Visualization
- srvyr-1.2.0 ‘dplyr’-Like Syntax for Summary Statistics of Survey Data
- ssgraph-1.15 Bayesian Graph Structure Learning using Spike-and-Slab Priors
- sva-3.48.0 Surrogate Variable Analysis
- systemPipeR-2.6.1 systemPipeR: NGS workflow and report generation environment
- tables-0.9.17 Formula-Driven Table Generation
- tergmLite-2.6.1 Fast Simulation of Simple Temporal Exponential Random Graph
Models
- text2vec-0.6.3 Modern Text Mining Framework for R
- tidymodels-1.1.0 Easily Install and Load the ‘Tidymodels’ Packages
- tidyposterior-1.0.0 Bayesian Analysis to Compare Models using Resampling Statistics
- tidypredict-0.5 Run Predictions Inside the Database
- tilingArray-1.78.0 Transcript mapping with high-density oligonucleotide tiling arrays
- timeSeries-4030.106 Financial Time Series Objects (Rmetrics)
- tkWidgets-1.78.0 R based tk widgets
- treeio-1.24.1 Base Classes and Functions for Phylogenetic Tree Input and Output
- tune-1.1.1 Tidy Tuning Tools
- udunits2-0.13.2.1 Udunits-2 Bindings for R
- uwot-0.1.14 The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
- venn-1.11 Draw Venn Diagrams
- vimp-2.3.1 Perform Inference on Algorithm-Agnostic Variable Importance
- vsn-3.68.0 Variance stabilization and calibration for microarray data
- warp-0.2.0 Group Dates
- wavethresh-4.7.2 Wavelets Statistics and Transforms
- webp-1.1.0 A New Format for Lossless and Lossy Image Compression
- widgetTools-1.78.0 Creates an interactive tcltk widget
- workflows-1.1.3 Modeling Workflows
- workflowsets-1.0.1 Create a Collection of ‘tidymodels’ Workflows
- xCell 1.1.0 [CRAN]
- xmlparsedata-1.0.5 Parse Data of ‘R’ Code as an ‘XML’ Tree
- yardstick-1.2.0 Tidy Characterizations of Model Performance
- zCompositions-1.4.0-1 Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Sets
- zlibbioc-1.46.0 An R packaged zlib-1.2.5