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

## Documentation for package ‘RcisTarget’ version 1.29.0

- 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