chipenrich

Gene Set Enrichment For ChIP-seq Peak Data

Bioconductor version: 3.23 · Package version: 2.36.0

ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("chipenrich")

Details

Maintainer	Kai Wang <wangdaha@umich.edu>
Author	Ryan P. Welch [aut, cph], Chee Lee [aut], Raymond G. Cavalcante [aut], Kai Wang [cre], Chris Lee [aut], Laura J. Scott [ths], Maureen A. Sartor [ths]
License	GPL-3
Downloads rank	458
Source branch	RELEASE_3_23
biocViews	ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, ImmunoOncology, Regression, Software

Documentation

chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

Download

Source package

Dependencies

Depends: R (>= 3.4.0)

Imports: AnnotationDbi, BiocGenerics, chipenrich.data, Seqinfo, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils

Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat