Man pages for girafe
Genome Intervals and Read Alignments for Functional Exploration
| agiFromBam | Create AlignedGenomeIntervals objects from BAM files. |
| AlignedGenomeIntervals-class | Class 'AlignedGenomeIntervals' |
| countReadsAnnotated | Sum up aligned reads per category of genome feature |
| fracOverlap | Retrieve intervals overlapping by fraction of width |
| getFeatureCounts | get the read counts for a supplied set of genomic features |
| girafe-internal | Internal girafe functions |
| intPhred | Extract integer Phred score values from FastQ data |
| medianByPosition | Compute median quality for each nucleotide position |
| negbinomsig | assess significance of sliding-window read counts |
| perWindow | Investigate aligned reads in genome intervals with sliding... |
| plotAligned | Visualise reads aligned to genome intervals |
| plotnegbinomfit | Plot Negative Binomial Fit |
| plotReads | Function to plot aligned reads along the chromosome |
| reduce-extras | Auxiliary methods for Function reduce in Package 'girafe' |
| trimAdapter | Remove 3' adapter contamination |
| weightedConsensusMatrix | compute weighted consensus matrix |
| whichNearestMethods | Methods for function 'which_nearest' and genome intervals |
