Package: RcisTarget
Type: Package
Title: RcisTarget Identify transcription factor binding motifs enriched
        on a list of genes or genomic regions
Version: 1.28.1
Date: 2024-03-02
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@kuleuven.be>
Description: 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).
URL: http://scenic.aertslab.org
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
Enhances: doMC, doRNG
Suggests: Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach,
        gplots, rtracklayer, igraph, knitr,
        RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat,
        visNetwork
License: GPL-3
BugReports: https://github.com/aertslab/RcisTarget/issues
biocViews: GeneRegulation, MotifAnnotation, Transcriptomics,
        Transcription, GeneSetEnrichment, GeneTarget
LazyData: FALSE
VignetteBuilder: knitr
RoxygenNote: 7.2.1
git_url: https://git.bioconductor.org/packages/RcisTarget
git_branch: RELEASE_3_21
git_last_commit: d3afd22
git_last_commit_date: 2025-05-08
Repository: Bioconductor 3.21
Date/Publication: 2025-05-08
NeedsCompilation: no
Packaged: 2025-05-09 01:53:45 UTC; biocbuild
Built: R 4.5.0; ; 2025-05-09 13:46:55 UTC; windows
