chipenrich
This is the released version of chipenrich; for the devel version, see chipenrich.
Gene Set Enrichment For ChIP-seq Peak Data
Bioconductor version: Release (3.23)
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.
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]
Maintainer: Kai Wang <wangdaha at umich.edu>
citation("chipenrich")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("chipenrich")
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("chipenrich")| chipenrich_vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, ImmunoOncology, Regression, Software |
| Version | 2.36.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 years) |
| License | GPL-3 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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 | chipenrich_2.36.0.tar.gz |
| Windows Binary (x86_64) | chipenrich_2.36.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | chipenrich_2.36.0.tgz |
| macOS Binary (sonoma-arm64) | chipenrich_2.36.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/chipenrich |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/chipenrich |
| Bioc Package Browser | https://code.bioconductor.org/browse/chipenrich/ |
| Package Short Url | https://bioconductor.org/packages/chipenrich/ |
| Package Downloads Report | Download Stats |