csaw
ChIP-Seq Analysis with Windows
Bioconductor version: 3.23 · Package version: 1.46.0
Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("csaw")Details
| Maintainer | Aaron Lun <infinite.monkeys.with.keyboards@gmail.com> |
| Author | Aaron Lun [aut, cre], Gordon Smyth [aut] |
| License | GPL-3 |
| System Requirements | C++11, GNU make |
| Downloads rank | 1144 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | csaw_1.46.0.tar.gz |
| Windows binary (x86_64) | csaw_1.46.0.zip |
| macOS binary (arm64) | csaw_1.46.0.tgz |
| macOS binary (x86_64) | csaw_1.46.0.tgz |
Dependencies
Depends: R (>= 3.5.0), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1)
Imports: Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, Seqinfo, stats, BiocParallel, metapod, utils
Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager