Package: RcisTarget
Type: Package
Title: RcisTarget Identify transcription factor binding motifs enriched
        on a list of genes or genomic regions
Version: 1.23.1
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
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://blaserlab.r-universe.dev
Date/Publication: 2024-03-04 10:41:33 UTC
RemoteUrl: https://github.com/aertslab/RcisTarget
RemoteRef: HEAD
RemoteSha: cddbff8ccb685557d25b821953ba5e1750f3174a
NeedsCompilation: no
Packaged: 2026-10-05 09:52:54 UTC; root