DiffBind

This is the released version of DiffBind; for the devel version, see DiffBind.

Differential Binding Analysis of ChIP-Seq Peak Data

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DOI: 10.18129/B9.bioc.DiffBind

Bioconductor version: Release (3.22)

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 <bioconductor at starkhome.com>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("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")

DiffBind: Differential binding analysis of ChIP-Seq peak data PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ATACSeq, BiomedicalInformatics, CellBiology, ChIPSeq, DNaseSeq, DifferentialMethylation, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, MethylSeq, MultipleComparison, Normalization, PeakDetection, RIPSeq, ReportWriting, Sequencing, Software

Version 3.20.0

In Bioconductor since BioC 2.9 (R-2.14) (14 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(>= 2.13.1), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP

System Requirements GNU make

URL https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/DiffBind

Suggests BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid

Linking To Rhtslib(>= 1.99.1), Rcpp

Enhances

Depends On Me vulcan

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package DiffBind_3.20.0.tar.gz

Windows Binary (x86_64) DiffBind_3.19.0.zip (64-bit only)

macOS Binary (x86_64) DiffBind_3.20.0.tgz

macOS Binary (arm64) DiffBind_3.20.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/DiffBind

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DiffBind

Bioc Package Browser https://code.bioconductor.org/browse/DiffBind/

Package Short Url https://bioconductor.org/packages/DiffBind/

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