TFEA.ChIP

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see TFEA.ChIP.

Analyze Transcription Factor Enrichment


Bioconductor version: 3.7

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

Author: Laura Puente SantamarĂ­a, Luis del Peso

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

Citation (from within R, enter citation("TFEA.ChIP")):

Installation

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


if (!require("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")
Vignette Title HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, GeneRegulation, GeneSetEnrichment, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License Artistic-2.0
Depends R (>= 3.5), dplyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
Imports GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices, stats, utils, R.utils
System Requirements
URL
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Suggests knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, GSEABase, DESeq2, BiocGenerics
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package TFEA.ChIP_1.0.0.tar.gz
Windows Binary TFEA.ChIP_1.0.0.zip
Mac OS X 10.11 (El Capitan) TFEA.ChIP_1.0.0.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 https://bioconductor.org/packages/TFEA.ChIP/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive