TFEA.ChIP

TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment

Bioconductor version: 3.23 · Package version: 1.32.0

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

Installation

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

BiocManager::install("TFEA.ChIP")

Maintainer	Yosra Berrouayel <yosraberrouayel@gmail.com>
Author	Yosra Berrouayel [aut, cre] (ORCID: <https://orcid.org/0000-0002-0768-5933>), Laura Puente-Santamaria [aut], Luis del Peso [aut] (ORCID: <https://orcid.org/0000-0003-4014-5688>)
License	Artistic-2.0
URL	https://github.com/yberda/TFEA.ChIP
Bug Reports	https://github.com/yberda/TFEA.ChIP/issues
Downloads rank	417
Source branch	RELEASE_3_23
biocViews	ChIPSeq, ChipOnChip, GeneExpression, GeneRegulation, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics

Dependencies

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

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)

Reverse dependencies

Suggests Me (1): ChIPDBData