Package: gmapR 1.55.1

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:Cory Barr, Thomas Wu, Michael Lawrence

gmapR_1.55.1.tar.gz

gmapR_1.55.1.tgz(r-4.6-x86_64)gmapR_1.55.1.tgz(r-4.6-arm64)gmapR_1.55.1.tgz(r-4.5-x86_64)
gmapR_1.55.1.tar.gz(r-4.7-arm64)gmapR_1.55.1.tar.gz(r-4.7-x86_64)gmapR_1.55.1.tar.gz(r-4.6-arm64)gmapR_1.55.1.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gmapR/json (API)

# Install 'gmapR' in R:

install.packages('gmapR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

zlib– Compression library

On BioConductor:gmapR-1.55.1(bioc 3.24)gmapR-1.54.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

alignment zlib

5.12 score 94 scripts 2 mentions 24 exports 69 dependencies

Last updated from:fbd5ff0dde. Checks:1 ERROR, 7 WARNING, 1 OK, 5 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	601
linux-devel-arm64	WARNING	897
linux-devel-x86_64	WARNING	1068
source / vignettes	OK	1050
linux-release-arm64	WARNING	886
linux-release-x86_64	WARNING	1065
macos-release-arm64	WARNING	590
macos-release-x86_64	WARNING	1030
macos-oldrel-arm64	FAIL	263
macos-oldrel-x86_64	WARNING	1927
windows-devel	FAIL	189
windows-release	FAIL	192
windows-oldrel	FAIL	203
wasm-release	FAIL	301

Exports:bam_tally bamPaths BamTallyParam cmetindex directory genome getSeq gmap GmapGenome GmapGenomeDirectory GmapParam GmapSnpDirectory GmapSnps gsnap GsnapOutput GsnapParam makeGmapGenomePackage path seqinfo snps<-spliceSites<-TP53Genome TP53Which variantSummary

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys VariantAnnotation vctrs XML XVector yaml

gmapR

Rendered fromgmapR.Rnwusingutils::Sweave

Last update: 2018-08-30
Started: 2012-08-02

Citation

Development and contributors

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