:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-gmapr' .. highlight: bash bioconductor-gmapr ================== .. conda:recipe:: bioconductor-gmapr :replaces_section_title: :noindex: An R interface to the GMAP\/GSNAP\/GSTRUCT suite :homepage: https://bioconductor.org/packages/3.18/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. .. conda:package:: bioconductor-gmapr |downloads_bioconductor-gmapr| |docker_bioconductor-gmapr| :versions: .. raw:: html
1.44.0-01.42.0-01.40.0-11.40.0-01.36.0-21.36.0-11.36.0-01.34.0-01.32.0-2 ``1.44.0-0``,  ``1.42.0-0``,  ``1.40.0-1``,  ``1.40.0-0``,  ``1.36.0-2``,  ``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`` .. raw:: html
:depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0a0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-biostrings: ``>=2.70.1,<2.71.0a0`` :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0`` :depends bioconductor-bsgenome: ``>=1.70.1,<1.71.0a0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomeinfodb: ``>=1.38.1,<1.39.0a0`` :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0a0`` :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicfeatures: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0a0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0a0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0`` :depends bioconductor-variantannotation: ``>=1.48.0,<1.49.0`` :depends bioconductor-variantannotation: ``>=1.48.1,<1.49.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends r-base: ``>=4.3,<4.4.0a0`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 quay.io/biocontainers/bioconductor-gmapr: (see `bioconductor-gmapr/tags`_ for valid values for ````) .. |downloads_bioconductor-gmapr| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-gmapr.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-gmapr :alt: (downloads) .. |docker_bioconductor-gmapr| image:: https://quay.io/repository/biocontainers/bioconductor-gmapr/status :target: https://quay.io/repository/biocontainers/bioconductor-gmapr .. _`bioconductor-gmapr/tags`: https://quay.io/repository/biocontainers/bioconductor-gmapr?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-gmapr/README.html