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
Bioconductor version: Development (3.22)
Package to analyze transcription factor enrichment in a gene set using data from ChIP-Seq experiments.
Author: Yosra Berrouayel [aut, cre]
, Laura Puente-Santamaria [aut], Luis del Peso [aut]
Maintainer: Yosra Berrouayel <yosraberrouayel at gmail.com>
citation("TFEA.ChIP")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, ChipOnChip, GeneExpression, GeneRegulation, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Version | 1.29.4 |
| 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 |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TFEA.ChIP_1.29.4.tar.gz |
| Windows Binary (x86_64) | TFEA.ChIP_1.29.1.zip |
| macOS Binary (x86_64) | TFEA.ChIP_1.29.4.tgz |
| macOS Binary (arm64) | TFEA.ChIP_1.29.4.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 |