This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RcisTarget.
Bioconductor version: 3.9
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: Sara Aibar <sara.aibar at kuleuven.vib.be>
Citation (from within R,
enter citation("RcisTarget")
):
To install this package, start R (version "3.6") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("RcisTarget")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RcisTarget")
HTML | R Script | RcisTarget: Transcription factor binding motif enrichment |
Reference Manual | ||
Text | NEWS |
biocViews | GeneRegulation, GeneSetEnrichment, GeneTarget, MotifAnnotation, Software, Transcription, Transcriptomics |
Version | 1.4.0 |
In Bioconductor since | BioC 3.7 (R-3.5) (1.5 years) |
License | GPL-3 |
Depends | R (>= 3.4) |
Imports | AUCell(>= 1.1.6), BiocGenerics, data.table, feather, graphics, GSEABase, methods, R.utils, stats, SummarizedExperiment, utils |
LinkingTo | |
Suggests | Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork |
SystemRequirements | |
Enhances | doMC, doRNG, zoo |
URL | http://scenic.aertslab.org |
BugReports | https://github.com/aertslab/RcisTarget/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | RcisTarget_1.4.0.tar.gz |
Windows Binary | RcisTarget_1.4.0.zip |
Mac OS X 10.11 (El Capitan) | RcisTarget_1.4.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/RcisTarget |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RcisTarget |
Package Short Url | https://bioconductor.org/packages/RcisTarget/ |
Package Downloads Report | Download Stats |
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