Man pages for GoekeLab/proActiv
Estimate Promoter Activity from RNA-Seq data
| boxplotPromoters | Visualizes promoter activity and gene expression with... |
| calculateJunctionReadCounts | Calculate the total number of junction reads overlapping with... |
| calculatePromoterReadCounts | Calculate the promoter read counts using junction read counts... |
| getAbsolutePromoterActivity | Prepare the absolute promoter activity table including the... |
| getAlternativePromoters | Identifies alternative promoters. |
| getGeneExpression | Prepare the gene expression table including the gene ids |
| getRelativePromoterActivity | Prepare the relative promoter activity table including the... |
| integrateProactiv | Integrate multiple proActiv runs |
| normalizePromoterReadCounts | Normalize promoter read counts using DESeq2 |
| plotHeatmap | Visualizes heatmap of features for samples |
| plotPCA | Performs principal component analysis |
| preparePromoterAnnotation | Prepares promoter annotation from a gtf or txdb |
| proActiv | Estimates promoter counts and activity in a single command |
| PromoterAnnotation-class | S4 class for promoter annotation data for a specific... |
| promoterAnnotation.gencode.v34.subset | Promoter annotation for Gencode.v34 (subset) |
| reexports | Objects exported from other packages |
