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| as.list-method | Class '"BamTallyParam"' |
| bamPaths-method | Class '"GsnapOutput"' |
| BamTallyParam | Class '"BamTallyParam"' |
| BamTallyParam-class | Class '"BamTallyParam"' |
| bam_tally | Per-position Alignment Summaries |
| bam_tally-method | Per-position Alignment Summaries |
| bam_tally-methods | Per-position Alignment Summaries |
| cmetindex | Call the cmetindex command |
| coerce-method | Class '"BamTallyParam"' |
| coerce-method | Class '"GmapGenome"' |
| directory | Get the Path to the Location on Disk from a gmapR Class |
| directory-method | Class '"GmapSnps"' |
| genome-method | Class '"GmapGenome"' |
| genome-method | Class '"GmapGenomeDirectory"' |
| genome-method | Per-position Alignment Summaries |
| getSeq-method | Class '"GmapGenome"' |
| GmapGenome | Class '"GmapGenome"' |
| GmapGenome-class | Class '"GmapGenome"' |
| GmapGenomeDirectory | Class '"GmapGenomeDirectory"' |
| GmapGenomeDirectory-class | Class '"GmapGenomeDirectory"' |
| GmapSnpDirectory | Class '"GmapSnpDirectory"' |
| GmapSnpDirectory-class | Class '"GmapSnpDirectory"' |
| GmapSnps | Class '"GmapSnps"' |
| GmapSnps-class | Class '"GmapSnps"' |
| gmap_build-method | Build Gmap/Gsnap Genome |
| gmap_build-methods | Build Gmap/Gsnap Genome |
| gsnap | Align a Set of Reads Using the GSNAP Aligner |
| gsnap-method | Align a Set of Reads Using the GSNAP Aligner |
| gsnap-methods | Align a Set of Reads Using the GSNAP Aligner |
| GsnapOutput | Class '"GsnapOutput"' |
| GsnapOutput-class | Class '"GsnapOutput"' |
| GsnapParam | Class '"GsnapParam"' |
| GsnapParam-class | Class '"GsnapParam"' |
| length-method | Class '"GmapSnpDirectory"' |
| makeGmapGenomePackage | Function to create a GmapGenome package from a GmapGenome object |
| names-method | Class '"GmapSnpDirectory"' |
| path-method | Class '"GmapGenome"' |
| path-method | Class '"GmapGenomeDirectory"' |
| path-method | Class '"GmapSnpDirectory"' |
| path-method | Class '"GsnapOutput"' |
| path-method | gmapR2 internals |
| seqinfo-method | Class '"GmapGenome"' |
| snps<- | Class '"GmapGenome"' |
| snps<--method | Class '"GmapGenome"' |
| snps<--method | Class '"GmapSnpDirectory"' |
| spliceSites<- | Class '"GmapGenome"' |
| spliceSites<--method | Class '"GmapGenome"' |
| TP53Genome | Demo genome around TP53 |
| TP53Which | Demo genome around TP53 |
| variantSummary | Per-position Alignment Summaries |
| [[<--method | Class '"GmapSnpDirectory"' |