recipe bioconductor-gmapr

An R interface to the GMAP/GSNAP/GSTRUCT suite

Homepage

https://bioconductor.org/packages/3.13/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

1.34.0-0,  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 >=2.52.0,<2.53.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-bsgenome >=1.60.0,<1.61.0

• bioconductor-genomeinfodb >=1.28.0,<1.29.0

• bioconductor-genomicalignments >=1.28.0,<1.29.0

• bioconductor-genomicfeatures >=1.44.0,<1.45.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-rsamtools >=2.8.0,<2.9.0

• bioconductor-rtracklayer >=1.52.0,<1.53.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-variantannotation >=1.38.0,<1.39.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=9.3.0

• liblapack >=3.8.0,<4.0a0

• r-base >=4.1,<4.2.0a0

Required By

• bioconductor-mmappr2

• bioconductor-htseqgenie

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>)

Link to this page

Render an badge with the following MarkDown:

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