Man pages for dnzdmrcgl/proActivTest
Estimate Promoter Activity from RNA-Seq data
| calculateJunctionReadCounts | Calculate the total number of junction reads overlapping with... |
| calculatePromoterReadCounts | Calculate the promoter read counts using junction read counts... |
| exonReducedRanges | Reduced exon ranges for the first exons of each gene to... |
| getAbsolutePromoterActivity | Prepare the absolute promoter activity table including the... |
| getGeneExpression | Prepare the gene expression table including the gene ids |
| getRelativePromoterActivity | Prepare the relative promoter activity table including the... |
| getUnannotatedReducedExonRanges | Get the reduced first exon ranges without metadata for the... |
| intronRanges.annotated | The intron ranges annotated with the promoter information. |
| normalizePromoterReadCounts | Normalize promoter read counts using DESeq2 |
| prepareAnnotatedIntronRanges | Prepare the annotated intron ranges for the annotating txdb... |
| prepareAnnotatedReducedExonRanges | Prepare the reduced exon ranges for each promoter using the... |
| preparePromoterCoordinates | Retrieve promoter coordinates (TSS) for each promoter with... |
| preparePromoterIdMapping | Prepare the id mapping between transcript ids, names, TSS... |
| promoterCoordinates | Transcription start site coordinates for each promoter... |
| promoterIdMapping | The id mapping between transcript ids, names, TSS ids,... |
