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RcisTarget
This is thereleased version of RcisTarget; for the devel version, seeRcisTarget.
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("RcisTarget")For older versions of R, please refer to the appropriateBioconductor 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 | 1.29.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (7.5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | RcisTarget_1.29.0.tar.gz |
| Windows Binary (x86_64) | RcisTarget_1.29.0.zip |
| macOS Binary (x86_64) | RcisTarget_1.29.0.tgz |
| macOS Binary (arm64) | RcisTarget_1.29.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RcisTarget |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RcisTarget |
| Bioc Package Browser | https://code.bioconductor.org/browse/RcisTarget/ |
| Package Short Url | https://bioconductor.org/packages/RcisTarget/ |
| Package Downloads Report | Download Stats |