TFEA.ChIP

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

TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment

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DOI: 10.18129/B9.bioc.TFEA.ChIP

Bioconductor version: Development (3.23)

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

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

Maintainer: Yosra Berrouayel <yosraberrouayel at gmail.com>

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

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, ChipOnChip, GeneExpression, GeneRegulation, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics

Version 1.31.0

In Bioconductor since BioC 3.7 (R-3.5) (7.5 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)

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Package Archives

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

Source Package TFEA.ChIP_1.31.0.tar.gz

Windows Binary (x86_64) TFEA.ChIP_1.31.0.zip (64-bit only)

macOS Binary (x86_64)

macOS Binary (arm64)

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/

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