gmapR
An R interface to the GMAP/GSNAP/GSTRUCT suite
Bioconductor version: 3.23 · Package version: 1.54.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("gmapR")Details
| Maintainer | Michael Lawrence <lawremi@gmail.com> |
| Author | Cory Barr, Thomas Wu, Michael Lawrence |
| License | Artistic-2.0 |
| Downloads rank | 498 |
| Source branch | RELEASE_3_23 |
| biocViews | Alignment, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | gmapR_1.54.0.tar.gz |
| macOS binary (arm64) | gmapR_1.54.0.tgz |
| macOS binary (x86_64) | gmapR_1.54.0.tgz |
Dependencies
Depends: R (>= 2.15.0), methods, Seqinfo, GenomicRanges (>= 1.61.1), Rsamtools (>= 1.31.2)
Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel, BiocIO
Suggests: GenomeInfoDb, RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
Reverse dependencies
Suggests Me (2): VariantTools, VariantToolsData