DiffBind
Differential Binding Analysis of ChIP-Seq Peak Data
Bioconductor version: 3.23 · Package version: 3.22.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DiffBind")Details
| Maintainer | Rory Stark <bioconductor@starkhome.com> |
| Author | Rory Stark [aut, cre], Gord Brown [aut] |
| License | Artistic-2.0 |
| URL | https://bioconductor.org/packages/DiffBind/ |
| System Requirements | GNU make |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ATACSeq, BiomedicalInformatics, CellBiology, ChIPSeq, DNaseSeq, DifferentialMethylation, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, MethylSeq, MultipleComparison, Normalization, PeakDetection, RIPSeq, ReportWriting, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/DiffBind/ |
Citation
From within R, enter citation("DiffBind"):
Rory Stark, Gord Brown. DiffBind: Differential Binding Analysis of ChIP-Seq Peak Data. doi:10.18129/B9.bioc.DiffBind, R package version 3.22.2, https://bioconductor.org/packages/DiffBind.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | DiffBind_3.22.2.tar.gz |
| Windows binary (x86_64) | DiffBind_3.22.2.zip |
| macOS binary (arm64) | DiffBind_3.22.2.tgz |
| macOS binary (x86_64) | DiffBind_3.22.2.tgz |
Dependencies
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
LinkingTo: Rhtslib (>= 1.99.1), Rcpp
Suggests: BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, rtracklayer, grid