TFEA.ChIP

DOI: 10.18129/B9.bioc.TFEA.ChIP    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see TFEA.ChIP.

Analyze Transcription Factor Enrichment

Bioconductor version: 3.8

Package to analize transcription factor enrichment in a gene set using data from ChIP-Seq experiments.

Author: Laura Puente Santamaría, Luis del Peso

Maintainer: Laura Puente Santamaría <lpsantamaria at iib.uam.es>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("TFEA.ChIP")

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("TFEA.ChIP")

 

HTML	R Script	Vignette Title
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, GeneRegulation, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version	1.2.3
In Bioconductor since	BioC 3.7 (R-3.5) (1 year)
License	Artistic-2.0
Depends	R (>= 3.3), dplyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
Imports	GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices, stats, utils, R.utils
LinkingTo
Suggests	knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, GSEABase, DESeq2, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	TFEA.ChIP_1.2.3.tar.gz
Windows Binary	TFEA.ChIP_1.2.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	TFEA.ChIP_1.2.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TFEA.ChIP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TFEA.ChIP
Package Short Url	http://bioconductor.org/packages/TFEA.ChIP/
Package Downloads Report	Download Stats