Package: RcisTarget 1.25.0

Gert Hulselmans

RcisTarget: RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

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).

Authors:Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of Computational Biology. VIB-KU Leuven Center for Brain & Disease Research. Leuven, Belgium

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Bug tracker:https://github.com/aertslab/rcistarget/issues

On BioConductor:RcisTarget-1.25.0(bioc 3.20)RcisTarget-1.24.0(bioc 3.19)

bioconductor-package

26 exports 0.91 score 116 dependencies 55 mentions

Last updated 2 months agofrom:0e77059dc5

Exports:addLogoaddMotifAnnotationaddSignificantGenesaucScorescalcAUCcisTargetcolnamesconvertToTargetRegionsgetAUCgetColumnNamesgetDbRegionsLocgetMaxRankgetMotifAnnotationgetNumColsInDBgetRankinggetRowNamesgetSignificantGenesimportAnnotationsimportRankingsncolnrowrankingRcisTargetreRankrownamesshowshowLogo

Dependencies:abindannotateAnnotationDbiarrowaskpassassertthatAUCellbase64encBiobaseBiocGenericsBiostringsbitbit64blobbslibcachemclicolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegraphGSEABasegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTkernlabknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemixtoolsmunsellnlmeopensslpillarpkgconfigplogrplotlypngpromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcpprlangrmarkdownRSQLiteS4ArraysS4VectorssassscalessegmentedSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryamlzlibbioczoo