DiffBind
This is thereleased version of DiffBind; for the devel version, seeDiffBind.
Differential Binding Analysis of ChIP-Seq Peak Data
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 appropriateBioconductor 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 | 3.20.0 |
| 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 |
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 | vulcan |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | DiffBind_3.20.0.tar.gz |
| Windows Binary (x86_64) | DiffBind_3.20.0.zip |
| 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/ |
| Package Downloads Report | Download Stats |