Package Recipe 'bioconductor-gmapr'

recipe bioconductor-gmapr

An R interface to the GMAP/GSNAP/GSTRUCT suite

Homepage: https://bioconductor.org/packages/3.14/bioc/html/gmapR.html
License: Artistic-2.0
Recipe: /bioconductor-gmapr/meta.yaml

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.

package bioconductor-gmapr¶

Versions

1.36.0-1, 1.36.0-0, 1.34.0-0, 1.32.0-2, 1.32.0-1, 1.32.0-0, 1.30.0-0, 1.28.0-0, 1.26.0-1,

1.36.0-1, 1.36.0-0, 1.34.0-0, 1.32.0-2, 1.32.0-1, 1.32.0-0, 1.30.0-0, 1.28.0-0, 1.26.0-1, 1.24.1-0

Depends

bioconductor-biobase >=2.54.0,<2.55.0
bioconductor-biocgenerics >=0.40.0,<0.41.0
bioconductor-biocparallel >=1.28.0,<1.29.0
bioconductor-biostrings >=2.62.0,<2.63.0
bioconductor-bsgenome >=1.62.0,<1.63.0
bioconductor-genomeinfodb >=1.30.0,<1.31.0
bioconductor-genomicalignments >=1.30.0,<1.31.0
bioconductor-genomicfeatures >=1.46.0,<1.47.0
bioconductor-genomicranges >=1.46.0,<1.47.0
bioconductor-iranges >=2.28.0,<2.29.0
bioconductor-rsamtools >=2.10.0,<2.11.0
bioconductor-rtracklayer >=1.54.0,<1.55.0
bioconductor-s4vectors >=0.32.0,<0.33.0
bioconductor-variantannotation >=1.40.0,<1.41.0
libblas >=3.8.0,<4.0a0
libgcc-ng >=10.3.0
liblapack >=3.8.0,<4.0a0
r-base >=4.1,<4.2.0a0

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-gmapr

and update with:

conda update bioconductor-gmapr

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-gmapr:<tag>

(see bioconductor-gmapr/tags for valid values for <tag>)

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-gmapr/README.html)