Bioconductor packages
300 in Packages and libraries, most used first. Page 2 of 2.
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destiny Creates diffusion maps - lpsymphony Symphony integer linear programming solver in R
- DSS Dispersion shrinkage for sequencing data
- DMRcate Methylation array and sequencing spatial analysis methods
- tximeta Transcript Quantification Import with Automatic Metadata
- infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data
- ggcyto Visualize Cytometry data with ggplot
- Glimma Interactive visualizations for gene expression analysis
- survcomp Performance Assessment and Comparison for Survival Analysis
- RUVSeq Remove Unwanted Variation from RNA-Seq Data
- QFeatures Quantitative features for mass spectrometry data
- FlowSOM Using self-organizing maps for visualization and interpretation of cytometry data
- wateRmelon Illumina DNA methylation array normalization and metrics
- motifmatchr Fast Motif Matching in R
- missMethyl Analysing Illumina HumanMethylation BeadChip Data
- TCGAutils TCGA utility functions for data management
- Spectra Spectra Infrastructure for Mass Spectrometry Data
- TreeSummarizedExperiment TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
- zellkonverter Conversion Between scRNA-seq Objects
- alabaster.base Save Bioconductor Objects to File
- Mfuzz Soft clustering of omics time series data
- chromVAR Chromatin Variation Across Regions
- BeadDataPackR Compression of Illumina BeadArray data
- alabaster.se Load and Save SummarizedExperiments from File
- Wrench Wrench normalization for sparse count data
- methylKit DNA methylation analysis from high-throughput bisulfite sequencing results
- SeqArray Data management of large-scale whole-genome sequence variant calls using GDS files
- alabaster.matrix Load and Save Artifacts from File
- ANCOMBC Microbiome differential abudance and correlation analyses with bias correction
- plyranges A fluent interface for manipulating GenomicRanges
- minet Mutual Information NETworks
- motifStack Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
- bamsignals Extract read count signals from bam files
- fastseg fastseg - a fast segmentation algorithm
- variancePartition Quantify and interpret drivers of variation in multilevel gene expression experiments
- karyoploteR Plot customizable linear genomes displaying arbitrary data
- ropls PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
- MotifDb An Annotated Collection of Protein-DNA Binding Sequence Motifs
- IHW Independent Hypothesis Weighting
- decontam Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
- chipseq chipseq: A package for analyzing chipseq data
- ChAMP Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
- CytoML A GatingML Interface for Cross Platform Cytometry Data Sharing
- ArrayExpress Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
- alabaster.ranges Load and Save Ranges-related Artifacts from File
- alabaster.schemas Schemas for the Alabaster Framework
- CAMERA Collection of annotation related methods for mass spectrometry data
- zinbwave Zero-Inflated Negative Binomial Model for RNA-Seq Data
- Rdisop Decomposition of Isotopic Patterns
- gypsum Interface to the gypsum REST API
- baySeq Empirical Bayesian analysis of patterns of differential expression in count data
- quantsmooth Quantile smoothing and genomic visualization of array data
- GlobalAncova Global test for groups of variables via model comparisons
- MsFeatures Functionality for Mass Spectrometry Features
- ALDEx2 Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
- Icens NPMLE for Censored and Truncated Data
- Heatplus Heatmaps with row and/or column covariates and colored clusters
- affycoretools Functions useful for those doing repetitive analyses with Affymetrix GeneChips
- GENIE3 GEne Network Inference with Ensemble of trees
- MetaboCoreUtils Core Utils for Metabolomics Data
- SPIA Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
- NOISeq Exploratory analysis and differential expression for RNA-seq data
- GWASTools Tools for Genome Wide Association Studies
- PCAtools PCAtools: Everything Principal Components Analysis
- GreyListChIP Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
- genomation Summary, annotation and visualization of genomic data
- MultiDataSet Implementation of MultiDataSet and ResultSet
- singscore Rank-based single-sample gene set scoring method
- MLInterfaces Uniform interfaces to R machine learning procedures for data in Bioconductor containers
- SRAdb A compilation of metadata from NCBI SRA and tools
- RcisTarget RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions
- UCell Rank-based signature enrichment analysis for single-cell data
- EnrichedHeatmap Making Enriched Heatmaps
- tradeSeq trajectory-based differential expression analysis for sequencing data
- RankProd Rank Product method for identifying differentially expressed genes with application in meta-analysis
- dittoSeq User Friendly Single-Cell and Bulk RNA Sequencing Visualization
- RCy3 Functions to Access and Control Cytoscape
- densvis Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction
- safe Significance Analysis of Function and Expression
- EBSeq An R package for gene and isoform differential expression analysis of RNA-seq data
- RaggedExperiment Representation of Sparse Experiments and Assays Across Samples
- microRNA Data and functions for dealing with microRNAs
- ggtreeExtra An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
- piano Platform for integrative analysis of omics data
- seqPattern Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
- decoupleR decoupleR: Ensemble of computational methods to infer biological activities from omics data
- DEGseq Identify Differentially Expressed Genes from RNA-seq data
- QuasR Quantify and Annotate Short Reads in R
- PSMatch Handling and Managing Peptide Spectrum Matches
- gwascat representing and modeling data in the EMBL-EBI GWAS catalog
- viper Virtual Inference of Protein-activity by Enriched Regulon analysis
- ctc Cluster and Tree Conversion.
- celda CEllular Latent Dirichlet Allocation
- SeqVarTools Tools for variant data
- csaw ChIP-Seq Analysis with Windows
- GLAD Gain and Loss Analysis of DNA
- MSstats Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
- RTCGAToolbox A new tool for exporting TCGA Firehose data
- trackViewer A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of…
- annotatr Annotation of Genomic Regions to Genomic Annotations
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