Bioconductor packages
300 in Packages and libraries, most used first. Page 1 of 2.
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BiocGenerics S4 generic functions used in Bioconductor - S4Vectors Foundation of vector-like and list-like containers in Bioconductor
- IRanges Foundation of integer range manipulation in Bioconductor
- Biobase Biobase: Base functions for Bioconductor
- BiocVersion Set the appropriate version of Bioconductor packages
- GenomeInfoDb Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
- XVector Foundation of external vector representation and manipulation in Bioconductor
- Biostrings Efficient manipulation of biological strings
- GenomicRanges Representation and manipulation of genomic intervals
- DelayedArray A unified framework for working transparently with on-disk and in-memory array-like datasets
- SummarizedExperiment A container (S4 class) for matrix-like assays
- BiocParallel Bioconductor facilities for parallel evaluation
- AnnotationDbi Manipulation of SQLite-based annotations in Bioconductor
- zlibbioc An R packaged zlib-1.2.5
- limma Linear Models for Microarray and Omics Data
- MatrixGenerics S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
- Rsamtools Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
- rtracklayer R interface to genome annotation files and the UCSC genome browser
- biomaRt Interface to BioMart databases (i.e. Ensembl)
- KEGGREST Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
- GenomicAlignments Representation and manipulation of short genomic alignments
- annotate Annotation for microarrays
- flowCore flowCore: Basic structures for flow cytometry data
- DESeq2 Differential gene expression analysis based on the negative binomial distribution
- edgeR Empirical Analysis of Digital Gene Expression Data in R
- GenomicFeatures Query the gene models of a given organism/assembly
- genefilter genefilter: methods for filtering genes from high-throughput experiments
- Rhtslib HTSlib high-throughput sequencing library as an R package
- graph graph: A package to handle graph data structures
- rhdf5 R Interface to HDF5
- BiocFileCache Manage Files Across Sessions
- S4Arrays Foundation of array-like containers in Bioconductor
- SparseArray High-performance sparse data representation and manipulation in R
- Rhdf5lib hdf5 library as an R package
- preprocessCore A collection of pre-processing functions
- BSgenome Software infrastructure for efficient representation of full genomes and their SNPs
- clusterProfiler A Universal Enrichment Tool for Interpreting Omics Data
- geneplotter Graphics related functions for Bioconductor
- ggtree An R package for visualization of tree and annotation data
- HDF5Array HDF5 datasets as array-like objects in R
- multtest Resampling-based multiple hypothesis testing
- enrichplot Visualization of Functional Enrichment Result
- fgsea Fast Gene Set Enrichment Analysis
- qvalue Q-value estimation for false discovery rate control
- DOSE Disease Ontology Semantic and Enrichment analysis
- GEOquery Get data from NCBI Gene Expression Omnibus (GEO)
- rhdf5filters HDF5 Compression Filters
- treeio Base Classes and Functions for Phylogenetic Tree Input and Output
- SingleCellExperiment S4 Classes for Single Cell Data
- GOSemSim GO-terms Semantic Similarity Measures
- affy Methods for Affymetrix Oligonucleotide Arrays
- BiocNeighbors Nearest Neighbor Detection for Bioconductor Packages
- BiocIO Standard Input and Output for Bioconductor Packages
- VariantAnnotation Annotation of Genetic Variants
- impute impute: Imputation for microarray data
- DelayedMatrixStats Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
- ComplexHeatmap Make Complex Heatmaps
- ShortRead FASTQ input and manipulation
- beachmat Compiling Bioconductor to Handle Each Matrix Type
- Rgraphviz Provides plotting capabilities for R graph objects
- RBGL An interface to the BOOST graph library
- affyio Tools for parsing Affymetrix data files
- sparseMatrixStats Summary Statistics for Rows and Columns of Sparse Matrices
- AnnotationHub Client to access AnnotationHub resources
- ensembldb Utilities to create and use Ensembl-based annotation databases
- UCSC.utils Low-level utilities to retrieve data from the UCSC Genome Browser
- ProtGenerics Generic infrastructure for Bioconductor mass spectrometry packages
- BiocSingular Singular Value Decomposition for Bioconductor Packages
- GSEABase Gene set enrichment data structures and methods
- AnnotationFilter Facilities for Filtering Bioconductor Annotation Resources
- scuttle Legacy Utilities for Single-Cell RNA-Seq Analysis
- biovizBase Basic graphic utilities for visualization of genomic data.
- batchelor Single-Cell Batch Correction Methods
- sva Surrogate Variable Analysis
- ScaledMatrix Creating a DelayedMatrix of Scaled and Centered Values
- vsn Variance stabilization and calibration for microarray data
- scater Single-Cell Analysis Toolkit for Gene Expression Data in R
- mzR parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
- BiocStyle Standard styles for vignettes and other Bioconductor documents
- phyloseq Handling and analysis of high-throughput microbiome census data
- Gviz Plotting data and annotation information along genomic coordinates
- xcms LC-MS and GC-MS Data Analysis
- interactiveDisplayBase Base package for enabling powerful shiny web displays of Bioconductor objects
- minfi Analyze Illumina Infinium DNA methylation arrays
- dada2 Accurate, high-resolution sample inference from amplicon sequencing data
- Seqinfo A simple S4 class for storing basic information about a collection of genomic sequences
- ExperimentHub Client to access ExperimentHub resources
- pcaMethods A collection of PCA methods
- biomformat An interface package for the BIOM file format
- GSVA Gene Set Variation Analysis for Microarray and RNA-Seq Data
- scran Methods for Single-Cell RNA-Seq Data Analysis
- DNAcopy DNA Copy Number Data Analysis
- KEGGgraph KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
- pathview A tool set for pathway based data integration and visualization
- gcrma Background Adjustment Using Sequence Information
- EBImage Image processing and analysis toolbox for R
- biocViews Categorized views of R package repositories
- bluster Clustering Algorithms for Bioconductor
- ReactomePA Reactome Pathway Analysis
- MSnbase Base Functions and Classes for Mass Spectrometry and Proteomics
- marray Exploratory analysis for two-color spotted microarray data
- ResidualMatrix Creating a DelayedMatrix of Regression Residuals
- siggenes Multiple Testing using SAM and Efron's Empirical Bayes Approaches
- TCGAbiolinks TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
- OrganismDbi Software to enable the smooth interfacing of different database packages
- affyPLM Methods for fitting probe-level models
- illuminaio Parsing Illumina Microarray Output Files
- MeSHDbi DBI to construct MeSH-related package from sqlite file
- MultiAssayExperiment Software for the integration of multi-omics experiments in Bioconductor
- bumphunter Bump Hunter
- Category Category Analysis
- topGO Enrichment Analysis for Gene Ontology
- ggbio Visualization tools for genomic data
- GOstats Tools for manipulating GO and microarrays
- AnnotationForge Tools for building SQLite-based annotation data packages
- tximport Import and summarize transcript-level estimates for transcript- and gene-level analysis
- cummeRbund Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
- apeglm Approximate posterior estimation for GLM coefficients
- EnhancedVolcano Publication-ready volcano plots with enhanced colouring and labeling
- DirichletMultinomial Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
- metapod Meta-Analyses on P-Values of Differential Analyses
- seqLogo Sequence logos for DNA sequence alignments
- oligo Preprocessing tools for oligonucleotide arrays
- BiocBaseUtils Utility and internal functions for Bioconductor packages
- monocle Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
- TFBSTools Software Package for Transcription Factor Binding Site (TFBS) Analysis
- assorthead Assorted Header-Only C++ Libraries
- snpStats SnpMatrix and XSnpMatrix classes and methods
- ChemmineR Cheminformatics Toolkit for R
- DynDoc Dynamic document tools
- SpatialExperiment S4 Class for Spatially Resolved -omics Data
- glmGamPoi Fit a Gamma-Poisson Generalized Linear Model
- mzID An mzIdentML parser for R
- dir.expiry Managing Expiration for Cache Directories
- SingleR Reference-Based Single-Cell RNA-Seq Annotation
- oligoClasses Classes for high-throughput arrays supported by oligo and crlmm
- ConsensusClusterPlus
- graphite GRAPH Interaction from pathway Topological Environment
- Rsubread Mapping, quantification and variant analysis of sequencing data
- lumi BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
- aroma.light Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
- affxparser Affymetrix File Parsing SDK
- cytolib C++ infrastructure for representing and interacting with the gated cytometry data
- DECIPHER Tools for curating, analyzing, and manipulating biological sequences
- mixOmics Omics Data Integration Project
- ChIPseeker ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
- EDASeq Exploratory Data Analysis and Normalization for RNA-Seq
- h5mread A fast HDF5 reader
- methylumi Handle Illumina methylation data
- annaffy Annotation tools for Affymetrix biological metadata
- flowViz Visualization for flow cytometry
- flowWorkspace Infrastructure for representing and interacting with gated and ungated cytometry data sets.
- RProtoBufLib C++ headers and static libraries of Protocol buffers
- MsCoreUtils Core Utils for Mass Spectrometry Data
- cigarillo Efficient manipulation of CIGAR strings
- DropletUtils Utilities for Handling Single-Cell Droplet Data
- gdsfmt R Interface to CoreArray Genomic Data Structure (GDS) Files
- maftools Summarize, Analyze and Visualize MAF Files
- DEXSeq Inference of differential exon usage in RNA-Seq
- basilisk Freezing Python Dependencies Inside Bioconductor Packages
- CNEr CNE Detection and Visualization
- regioneR Association analysis of genomic regions based on permutation tests
- BiocCheck Bioconductor-specific package checks
- ChIPpeakAnno Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of…
- pwalign Perform pairwise sequence alignments
- MassSpecWavelet Peak Detection for Mass Spectrometry data using wavelet-based algorithms
- ROC utilities for ROC, with microarray focus
- DiffBind Differential Binding Analysis of ChIP-Seq Peak Data
- ncdfFlow ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
- globaltest Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
- MAST Model-based Analysis of Single Cell Transcriptomics
- goseq Gene Ontology analyser for RNA-seq and other length biased data
- systemPipeR systemPipeR: A Multipurpose Workflow Management System for Reproducible Data Analysis
- SNPRelate Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
- widgetTools Creates an interactive tcltk widget
- bsseq Analyze, manage and store whole-genome methylation data
- msa Multiple Sequence Alignment
- tkWidgets R based tk widgets
- mosaics MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
- basilisk.utils Centralized Conda Installation for Bioconductor Packages
- AUCell AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
- metagenomeSeq Statistical analysis for sparse high-throughput sequencing
- flowStats Statistical methods for the analysis of flow cytometry data
- scDblFinder
- ReportingTools Tools for making reports in various formats
- microbiome Microbiome Analytics
- TrajectoryUtils Single-Cell Trajectory Analysis Utilities
- mia Microbiome analysis
- ChemmineOB R interface to a subset of OpenBabel functionalities
- flowClust Clustering for Flow Cytometry
- beadarray Quality assessment and low-level analysis for Illumina BeadArray data
- gage Generally Applicable Gene-set Enrichment for Pathway Analysis
- GenomicDataCommons NIH / NCI Genomic Data Commons Access
- STRINGdb STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis
- InteractionSet Base Classes for Storing Genomic Interaction Data
- arrayQualityMetrics Quality metrics report for microarray data sets
- openCyto Hierarchical Gating Pipeline for flow cytometry data
- txdbmaker Tools for making TxDb objects from genomic annotations
- GenomicFiles Distributed computing by file or by range
- ballgown Flexible, isoform-level differential expression analysis
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