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TFEA.ChIP

This is the development version of TFEA.ChIP; for the stable release version, see TFEA.ChIP.

Analyze Transcription Factor Enrichment


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
TFEA.ChIP: a tool kit for transcription factor enrichment HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, GeneRegulation, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.23.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License Artistic-2.0
Depends R (>= 3.5)
Imports GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices, dplyr, stats, utils, R.utils, methods, org.Hs.eg.db
System Requirements
URL
See More
Suggests knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit
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Package Archives

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

Source Package TFEA.ChIP_1.23.0.tar.gz
Windows Binary TFEA.ChIP_1.23.0.zip
macOS Binary (x86_64) TFEA.ChIP_1.23.0.tgz
macOS Binary (arm64) TFEA.ChIP_1.23.0.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
Bioc Package Browser https://code.bioconductor.org/browse/TFEA.ChIP/
Package Short Url https://bioconductor.org/packages/TFEA.ChIP/
Package Downloads Report Download Stats