Man pages for nzhang89/RiboSeeker
A Package for Ribosome Profiling Data Analysis and Visualization
| calcMetagene | Metagene matrix calculation |
| calcORFScore | ORFScore calculation |
| calcRPKM | Calculate RPKM |
| calcTransEff | Calculate translation efficiency |
| dot-calcMetagene | Calculate metagene matrix for fixed length regions |
| dot-calcMetageneStat | Calculate metagene column-wise summary statistics |
| dot-calcRelFreq | Convert to row-wise relative frequency |
| dot-clacMetageneRegion | Calculate metagene region |
| dot-filterSeqlevels | Filter seqlevels |
| dot-getCDSRegions | Get CDS start and end regions |
| dot-getFramePosPct | Calculate the percentage of positive elements for each row in... |
| dot-getORFScoreSign | Calculate ORFScore sign |
| dot-getRawORFScore | Calculate raw ORFScore |
| dot-now | Get current time |
| dot-plot_theme | Plot theme |
| dot-shift | Shift the 5'-end of reads of towards downstream position |
| dot-stdGRL | Standadize ORF GrangesList |
| dot-subsetMetagene | Subset metagene matrices |
| dot-trimORF | Trim ORF |
| loadBam | Load a BAM file |
| metagenePlot | Metagene plot |
| readGenomeDist | Genomic feature distribution of aligned reads |
| readGenomeDistPlot | Genomic feature distribution plot of aligned reads |
| readLengthDist | Read length distribution |
| readLengthDistPlot | Read length distribution plot |
| shiftReads | Shift the 5'-end of reads of towards downstream direction |
