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chipenrich
This is thereleased version of chipenrich; for the devel version, seechipenrich.
Gene Set Enrichment For ChIP-seq Peak Data
Bioconductor version: Release (3.22)
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")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("chipenrich")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("chipenrich")| chipenrich_vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq,Epigenetics,FunctionalGenomics,GeneSetEnrichment,HistoneModification,ImmunoOncology,Regression,Software |
| Version | 2.34.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (12 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
FollowInstallation instructions to use this package in your R session.
| Source Package | chipenrich_2.34.0.tar.gz |
| Windows Binary (x86_64) | chipenrich_2.34.0.zip |
| macOS Binary (x86_64) | chipenrich_2.34.0.tgz |
| macOS Binary (arm64) | chipenrich_2.34.0.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 |