TFEA.ChIP
TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment
Bioconductor version: 3.24 · Package version: 1.33.3
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")Details
| 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 | 666 |
| Source branch | devel |
| biocViews | ChIPSeq, ChipOnChip, GeneExpression, GeneRegulation, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | TFEA.ChIP_1.33.3.tar.gz |
| Windows binary (x86_64) | TFEA.ChIP_1.33.3.zip |
| macOS binary (arm64) | TFEA.ChIP_1.33.3.tgz |
| macOS binary (x86_64) | TFEA.ChIP_1.33.3.tgz |
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