BioConductor

gmapR 1.22.0

An R interface to the GMAP/GSNAP/GSTRUCT suite

Released Apr 30, 2018 by Michael Lawrence

This package cannot yet be used with Renjin it depends on other packages which are not available: rtracklayer 1.40.5, VariantAnnotation 1.26.1, BSgenome 1.48.0, and GenomicFeatures 1.32.2

Dependencies

rtracklayer 1.40.5 BSgenome 1.48.0 VariantAnnotation 1.26.1 GenomicFeatures 1.32.2 GenomeInfoDb 1.16.0 S4Vectors 0.18.3 BiocParallel 1.14.2 Rsamtools 1.32.3 Biobase 2.40.0 GenomicAlignments 1.16.0 Biostrings 2.48.0 GenomicRanges 1.32.6 BiocGenerics 0.26.0 IRanges 2.14.10

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.

Source

R
C

Release History