DiffBind

DOI: 10.18129/B9.bioc.DiffBind    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see DiffBind.

Differential Binding Analysis of ChIP-Seq Peak Data

Bioconductor version: 3.13

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Author: Rory Stark [aut, cre], Gord Brown [aut]

Maintainer: Rory Stark <rory.stark at cruk.cam.ac.uk>

Citation (from within R, enter citation("DiffBind")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DiffBind")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DiffBind")

 

PDF R Script DiffBind: Differential binding analysis of ChIP-Seq peak data
PDF   Reference Manual
Text   NEWS

Details

biocViews ATACSeq, BiomedicalInformatics, CellBiology, ChIPSeq, DNaseSeq, DifferentialMethylation, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, MethylSeq, MultipleComparison, Normalization, PeakDetection, RIPSeq, ReportWriting, Sequencing, Software
Version 3.2.7
In Bioconductor since BioC 2.9 (R-2.14) (10 years)
License Artistic-2.0
Depends R (>= 4.0), GenomicRanges, SummarizedExperiment
Imports RColorBrewer, amap, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools(>= 2.0), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP
LinkingTo Rhtslib(>= 1.15.3), Rcpp
Suggests BiocStyle, testthat, xtable
SystemRequirements GNU make
Enhances rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid
URL https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/DiffBind
Depends On Me ChIPQC, vulcan
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DiffBind_3.2.7.tar.gz
Windows Binary DiffBind_3.2.7.zip
macOS 10.13 (High Sierra) DiffBind_3.2.7.tgz
Source Repository git clone https://git.bioconductor.org/packages/DiffBind
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DiffBind
Package Short Url https://bioconductor.org/packages/DiffBind/
Package Downloads Report Download Stats

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