Package: RcisTarget 1.23.1
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:
RcisTarget_1.23.1.tar.gz
RcisTarget_1.23.1.zip(r-4.5)RcisTarget_1.23.1.zip(r-4.4)RcisTarget_1.23.1.zip(r-4.3)
RcisTarget_1.23.1.tgz(r-4.4-any)RcisTarget_1.23.1.tgz(r-4.3-any)
RcisTarget_1.23.1.tar.gz(r-4.5-noble)RcisTarget_1.23.1.tar.gz(r-4.4-noble)
RcisTarget_1.23.1.tgz(r-4.4-emscripten)RcisTarget_1.23.1.tgz(r-4.3-emscripten)
RcisTarget.pdf |RcisTarget.html✨
RcisTarget/json (API)
NEWS
# Install 'RcisTarget' in R: |
install.packages('RcisTarget', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/aertslab/rcistarget/issues
- dbRegionsLoc_hg19_v9 - Genomic location for the database regions
- motifAnnotations - Annotations of Motifs to TFs
- motifAnnotations - Annotations of Motifs to TFs
- motifAnnotations - Annotations of Motifs to TFs
- motifAnnotations_dmel_v8 - Annotations of Motifs to TFs
- motifAnnotations_dmel_v9 - Annotations of Motifs to TFs
- motifAnnotations_hgnc_v9 - Annotations of Motifs to TFs
- motifAnnotations_mgi_v9 - Annotations of Motifs to TFs
On BioConductor:RcisTarget-1.25.0(bioc 3.20)RcisTarget-1.24.0(bioc 3.19)
Last updated 6 months agofrom:cddbff8ccb. Checks:OK: 2 NOTE: 5. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 31 2024 |
R-4.5-win | NOTE | Aug 31 2024 |
R-4.5-linux | NOTE | Aug 31 2024 |
R-4.4-win | NOTE | Aug 31 2024 |
R-4.4-mac | NOTE | Aug 31 2024 |
R-4.3-win | NOTE | Aug 31 2024 |
R-4.3-mac | OK | Aug 31 2024 |
Exports:addLogoaddMotifAnnotationaddSignificantGenesaucScorescalcAUCcisTargetcolnamesconvertToTargetRegionsgetAUCgetColumnNamesgetDbRegionsLocgetMaxRankgetMotifAnnotationgetNumColsInDBgetRankinggetRowNamesgetSignificantGenesimportAnnotationsimportRankingsncolnrowrankingRcisTargetreRankrownamesshowshowLogo
Dependencies:abindannotateAnnotationDbiarrowaskpassassertthatAUCellbase64encBiobaseBiocGenericsBiostringsbitbit64blobbslibcachemclicolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegraphGSEABasegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTkernlabknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemixtoolsmunsellnlmeopensslpillarpkgconfigplogrplotlypngpromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcpprlangrmarkdownRSQLiteS4ArraysS4VectorssassscalessegmentedSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryamlzlibbioczoo
Motif enrichment in genomic regions
Rendered fromTutorial_AnalysisOfGenomicRegions.Rmd
usingknitr::rmarkdown
on Aug 31 2024.Last update: 2024-03-04
Started: 2021-03-24
Motif enrichment with background
Rendered fromTutorial_AnalysisWithBackground.Rmd
usingknitr::rmarkdown
on Aug 31 2024.Last update: 2022-04-05
Started: 2021-03-24
RcisTarget: Transcription factor binding motif enrichment
Rendered fromRcisTarget_MainTutorial.Rmd
usingknitr::rmarkdown
on Aug 31 2024.Last update: 2022-10-31
Started: 2021-03-24
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Add motif logo to RcisTarget results table | addLogo |
Add motif annotation | addMotifAnnotation |
Add significant genes | addSignificantGenes addSignificantGenes,character-method addSignificantGenes,GeneSet-method addSignificantGenes,GeneSetCollection-method addSignificantGenes,list-method getSignificantGenes getSignificantGenes,character-method getSignificantGenes,factor-method getSignificantGenes,GeneSet-method getSignificantGenes,GeneSetCollection-method getSignificantGenes,list-method |
Class to store the AUC scores for RcisTarget. | aucScores aucScores-class getAUC getAUC,aucScores-method show,aucScores-method |
Calculate AUC | calcAUC calcAUC,character-method calcAUC,GeneSet-method calcAUC,GeneSetCollection-method calcAUC,list-method |
cisTarget | cisTarget |
convertToTargetRegions | convertToTargetRegions |
Genomic location for the database regions | dbRegionsLoc dbRegionsLoc_hg19_v9 dbRegionsLoc_mm9_v9 |
Gets the region location for the given database IDs. | getDbRegionsLoc |
Get motif annotation | getMotifAnnotation |
Imports the annotations of motifs to transcription factors | importAnnotations |
Import the motif databases for RcisTarget. | getColumnNames getRowNames importRankings |
Annotations of Motifs to TFs | motifAnnotations motifAnnotations_dmel motifAnnotations_dmel_v8 motifAnnotations_dmel_v9 motifAnnotations_hgnc motifAnnotations_hgnc_v8 motifAnnotations_hgnc_v9 motifAnnotations_mgi motifAnnotations_mgi_v8 motifAnnotations_mgi_v9 |
Class to store the motif databases for RcisTarget. | colnames,rankingRcisTarget-method getMaxRank getMaxRank,rankingRcisTarget-method getNumColsInDB getNumColsInDB,rankingRcisTarget-method getRanking getRanking,rankingRcisTarget-method ncol,rankingRcisTarget-method nrow,rankingRcisTarget-method rankingRcisTarget rankingRcisTarget-class rownames,rankingRcisTarget-method show,rankingRcisTarget-method |
Re-rank RcisTarget ranking | reRank |
Show RcisTarget as HTML | showLogo |