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TFEA.ChIP

Analyze Transcription Factor Enrichment


Bioconductor version: Release (3.18)

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 "4.3") 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")
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 1.22.0
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
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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_1.22.0.tar.gz
Windows Binary TFEA.ChIP_1.22.0.zip (64-bit only)
macOS Binary (x86_64) TFEA.ChIP_1.22.0.tgz
macOS Binary (arm64) TFEA.ChIP_1.22.0.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