DiffBind

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see DiffBind.

Differential Binding Analysis of ChIP-Seq Peak Data

Bioconductor version: 3.14

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 (!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 3.4.11

In Bioconductor since BioC 2.9 (R-2.14) (12.5 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

System Requirements GNU make

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

Suggests BiocStyle, testthat, xtable

Linking To Rhtslib(>= 1.15.3), Rcpp

Enhances rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid

Depends On Me ChIPQC, vulcan

Imports Me

Suggests Me

Links To Me

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