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

---

Documentation for package ‘RcisTarget’ version 1.28.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

addLogo	Add motif logo to RcisTarget results table
addMotifAnnotation	Add motif annotation
addSignificantGenes	Add significant genes
addSignificantGenes-method	Add significant genes
aucScores	Class to store the AUC scores for RcisTarget.
aucScores-class	Class to store the AUC scores for RcisTarget.
calcAUC	Calculate AUC
calcAUC-method	Calculate AUC
cisTarget	cisTarget
colnames-method	Class to store the motif databases for RcisTarget.
convertToTargetRegions	convertToTargetRegions
dbRegionsLoc	Genomic location for the database regions
dbRegionsLoc_hg19_v9	Genomic location for the database regions
dbRegionsLoc_mm9_v9	Genomic location for the database regions
getAUC	Class to store the AUC scores for RcisTarget.
getAUC-method	Class to store the AUC scores for RcisTarget.
getColumnNames	Import the motif databases for RcisTarget.
getDbRegionsLoc	Gets the region location for the given database IDs.
getMaxRank	Class to store the motif databases for RcisTarget.
getMaxRank-method	Class to store the motif databases for RcisTarget.
getMotifAnnotation	Get motif annotation
getNumColsInDB	Class to store the motif databases for RcisTarget.
getNumColsInDB-method	Class to store the motif databases for RcisTarget.
getRanking	Class to store the motif databases for RcisTarget.
getRanking-method	Class to store the motif databases for RcisTarget.
getRowNames	Import the motif databases for RcisTarget.
getSignificantGenes	Add significant genes
getSignificantGenes-method	Add significant genes
importAnnotations	Imports the annotations of motifs to transcription factors
importRankings	Import the motif databases for RcisTarget.
motifAnnotations	Annotations of Motifs to TFs
motifAnnotations_dmel	Annotations of Motifs to TFs
motifAnnotations_dmel_v8	Annotations of Motifs to TFs
motifAnnotations_dmel_v9	Annotations of Motifs to TFs
motifAnnotations_hgnc	Annotations of Motifs to TFs
motifAnnotations_hgnc_v8	Annotations of Motifs to TFs
motifAnnotations_hgnc_v9	Annotations of Motifs to TFs
motifAnnotations_mgi	Annotations of Motifs to TFs
motifAnnotations_mgi_v8	Annotations of Motifs to TFs
motifAnnotations_mgi_v9	Annotations of Motifs to TFs
ncol-method	Class to store the motif databases for RcisTarget.
nrow-method	Class to store the motif databases for RcisTarget.
rankingRcisTarget	Class to store the motif databases for RcisTarget.
rankingRcisTarget-class	Class to store the motif databases for RcisTarget.
reRank	Re-rank RcisTarget ranking
rownames-method	Class to store the motif databases for RcisTarget.
show-method	Class to store the AUC scores for RcisTarget.
show-method	Class to store the motif databases for RcisTarget.
showLogo	Show RcisTarget as HTML