RcisTarget
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see RcisTarget.
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions
Bioconductor version: 3.19
RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).
Author: Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of Computational Biology. VIB-KU Leuven Center for Brain & Disease Research. Leuven, Belgium
Maintainer: Gert Hulselmans <Gert.Hulselmans at kuleuven.be>
citation("RcisTarget")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RcisTarget")
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("RcisTarget")| RcisTarget - on regions | HTML | R Script |
| RcisTarget - with background | HTML | R Script |
| RcisTarget: Transcription factor binding motif enrichment | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneRegulation, GeneSetEnrichment, GeneTarget, MotifAnnotation, Software, Transcription, Transcriptomics |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0) |
| Imports | AUCell(>= 1.1.6), BiocGenerics, data.table, graphics, GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr, tibble, GSEABase, methods, R.utils, stats, SummarizedExperiment, S4Vectors, utils, zoo |
| System Requirements | |
| URL | http://scenic.aertslab.org |
| Bug Reports | https://github.com/aertslab/RcisTarget/issues |
See More
| Suggests | Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, gplots, rtracklayer, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork |
| Linking To | |
| Enhances | doMC, doRNG |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RcisTarget_1.24.0.tar.gz |
| Windows Binary (x86_64) | RcisTarget_1.24.0.zip |
| macOS Binary (x86_64) | RcisTarget_1.24.0.tgz |
| macOS Binary (arm64) | RcisTarget_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RcisTarget |
| Source Repository (Developer Access) | git clone [email protected]:packages/RcisTarget |
| Bioc Package Browser | https://code.bioconductor.org/browse/RcisTarget/ |
| Package Short Url | https://bioconductor.org/packages/RcisTarget/ |
| Package Downloads Report | Download Stats |