DiffBind
Differential Binding Analysis of ChIP-Seq Peak Data
Bioconductor version: Release (3.19)
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 "4.4") 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 | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | ATACSeq, BiomedicalInformatics, CellBiology, ChIPSeq, DNaseSeq, DifferentialMethylation, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, MethylSeq, MultipleComparison, Normalization, PeakDetection, RIPSeq, ReportWriting, Sequencing, Software |
Version | 3.14.0 |
In Bioconductor since | BioC 2.9 (R-2.14) (13 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.
Source Package | DiffBind_3.14.0.tar.gz |
Windows Binary | DiffBind_3.14.0.zip |
macOS Binary (x86_64) | DiffBind_3.14.0.tgz |
macOS Binary (arm64) | DiffBind_3.14.0.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/ |
Package Downloads Report | Download Stats |