TFEA.ChIP

This is the released version of TFEA.ChIP; for the devel version, see TFEA.ChIP.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment

Bioconductor version: Release (3.23)

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

Author: Yosra Berrouayel [aut, cre] ORCID: 0000-0002-0768-5933 , Laura Puente-Santamaria [aut], Luis del Peso [aut] ORCID: 0000-0003-4014-5688

Maintainer: Yosra Berrouayel <yosraberrouayel at gmail.com>

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

Yosra Berrouayel, Laura Puente-Santamaria, Luis del Peso. TFEA.ChIP: TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment. doi:10.18129/B9.bioc.TFEA.ChIP, R package version 1.32.0, https://bioconductor.org/packages/TFEA.ChIP.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, ChipOnChip, GeneExpression, GeneRegulation, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version	1.32.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	GenomicRanges, IRanges, biomaRt, GenomicFeatures, GenomicRanges, grDevices, dplyr, stats, utils, R.utils, methods, org.Hs.eg.db, org.Mm.eg.db, rlang, ExperimentHub
System Requirements
URL	https://github.com/yberda/TFEA.ChIP
Bug Reports	https://github.com/yberda/TFEA.ChIP/issues

Suggests	knitr, rmarkdown, BiocStyle, S4Vectors, Seqinfo, meta, plotly, scales, tidyr, purrr, tibble, ggplot2, DESeq2, edgeR, limma, babelgene, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, RColorBrewer, RUnit, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	ChIPDBData
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	TFEA.ChIP_1.32.0.tar.gz
Windows Binary (x86_64)	TFEA.ChIP_1.32.0.zip
macOS Binary (big-sur-x86_64)	TFEA.ChIP_1.32.0.tgz
macOS Binary (sonoma-arm64)	TFEA.ChIP_1.32.0.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