recipe bioconductor-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.

package bioconductor-gmapr

(downloads) docker_bioconductor-gmapr



depends bioconductor-biobase:


depends bioconductor-biocgenerics:


depends bioconductor-biocparallel:


depends bioconductor-biostrings:


depends bioconductor-bsgenome:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicalignments:


depends bioconductor-genomicfeatures:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-rsamtools:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends bioconductor-variantannotation:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends r-base:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-gmapr

and update with::

   mamba update bioconductor-gmapr

To create a new environment, run:

mamba create --name myenvname bioconductor-gmapr

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

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

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