Package: gmapR 1.49.0
Michael Lawrence
gmapR: An R interface to the GMAP/GSNAP/GSTRUCT suite
GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.
Authors:
gmapR_1.49.0.tar.gz
gmapR_1.49.0.tar.gz(r-4.5-noble)gmapR_1.49.0.tar.gz(r-4.4-noble)
gmapR.pdf |gmapR.html✨
gmapR/json (API)
NEWS
| # Install 'gmapR' in R: |
| install.packages('gmapR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:gmapR-1.49.0(bioc 3.21)gmapR-1.48.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:fbb42aed1f. Checks:OK: 1 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 29 2024 |
Exports:bam_tallybamPathsBamTallyParamcmetindexdirectorygenomegetSeqgmapGmapGenomeGmapGenomeDirectoryGmapParamGmapSnpDirectoryGmapSnpsgsnapGsnapOutputGsnapParammakeGmapGenomePackagepathseqinfosnps<-spliceSites<-TP53GenomeTP53WhichvariantSummary
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Per-position Alignment Summaries | bam_tally bam_tally,BamFile-method bam_tally,character-method bam_tally,GmapBamReader-method bam_tally-methods genome,TallyIIT-method variantSummary |
| Class '"BamTallyParam"' | as.list,BamTallyParam-method BamTallyParam BamTallyParam-class coerce,BamTallyParam,list-method |
| Call the cmetindex command | cmetindex |
| Get the Path to the Location on Disk from a gmapR Class | directory |
| Build Gmap/Gsnap Genome | gmap_build,ANY,GmapGenome-method gmap_build,character,GmapGenome-method gmap_build,DNAStringSet,GmapGenome-method gmap_build-methods |
| Class '"GmapGenome"' | coerce,GmapGenome,DNAStringSet-method genome,GmapGenome-method getSeq,GmapGenome-method GmapGenome GmapGenome-class path,GmapGenome-method seqinfo,GmapGenome-method snps<- snps<-,GmapGenome,ANY,ANY-method spliceSites<- spliceSites<-,GmapGenome,GRangesList-method spliceSites<-,GmapGenome,TxDb-method |
| Class '"GmapGenomeDirectory"' | genome,GmapGenomeDirectory-method GmapGenomeDirectory GmapGenomeDirectory-class path,GmapGenomeDirectory-method path,NULL-method |
| Class '"GmapSnpDirectory"' | GmapSnpDirectory GmapSnpDirectory-class length,GmapSnpDirectory-method names,GmapSnpDirectory-method path,GmapSnpDirectory-method snps<-,GmapSnpDirectory,character,character-method snps<-,GmapSnpDirectory,character,VCF-method [[<-,GmapSnpDirectory,ANY,ANY-method |
| Class '"GmapSnps"' | directory,GmapSnps-method GmapSnps GmapSnps-class |
| Align a Set of Reads Using the GSNAP Aligner | gsnap gsnap,character,character_OR_NULL,GsnapParam-method gsnap-methods |
| Class '"GsnapOutput"' | bamPaths,GsnapOutput-method GsnapOutput GsnapOutput-class path,GsnapOutput-method |
| Class '"GsnapParam"' | GsnapParam GsnapParam-class |
| gmapR2 internals | path,GmapBamReader-method |
| Function to create a GmapGenome package from a GmapGenome object | makeGmapGenomePackage |
| Demo genome around TP53 | TP53Genome TP53Which |
