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Bioconductor - DiffBind (development version)

DiffBind

This is the development version of DiffBind; for the stable release version, see DiffBind.

Differential Binding Analysis of ChIP-Seq Peak Data

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 Details biocViews ATACSeq, BiomedicalInformatics, CellBiology, ChIPSeq, DNaseSeq, DifferentialMethylation, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, MethylSeq, MultipleComparison, Normalization, PeakDetection, RIPSeq, ReportWriting, Sequencing, Software Version 3.19.0 In Bioconductor since BioC 2.9 (R-2.14) (13.5 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(>= 2.13.1), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP System Requirements GNU make URL https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/DiffBind See More Suggests BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid Linking To Rhtslib(>= 1.99.1), Rcpp Enhances Depends On Me ChIPQC, 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.

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