:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-proteodisco' .. highlight: bash bioconductor-proteodisco ======================== .. conda:recipe:: bioconductor-proteodisco :replaces_section_title: :noindex: Generation of customized protein variant databases from genomic variants\, splice\-junctions and manual sequences :homepage: https://bioconductor.org/packages/3.18/bioc/html/ProteoDisco.html :license: GPL-3 :recipe: /`bioconductor-proteodisco `_/`meta.yaml `_ ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized \(variant\) protein databases based on user\-submitted genomic variants\, splice\-junctions\, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings. .. conda:package:: bioconductor-proteodisco |downloads_bioconductor-proteodisco| |docker_bioconductor-proteodisco| :versions: ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.0.0-0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-cleaver: ``>=1.40.0,<1.41.0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-variantannotation: ``>=1.48.0,<1.49.0`` :depends bioconductor-xvector: ``>=0.42.0,<0.43.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-checkmate: ``>=2.0.0`` :depends r-dplyr: ``>=1.0.6`` :depends r-parallellogger: ``>=2.0.1`` :depends r-plyr: ``>=1.8.6`` :depends r-rlang: ``>=0.4.11`` :depends r-tibble: ``>=3.1.2`` :depends r-tidyr: ``>=1.1.3`` :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-proteodisco and update with:: mamba update bioconductor-proteodisco To create a new environment, run:: mamba create --name myenvname bioconductor-proteodisco 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-proteodisco: (see `bioconductor-proteodisco/tags`_ for valid values for ````) .. |downloads_bioconductor-proteodisco| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-proteodisco.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-proteodisco :alt: (downloads) .. |docker_bioconductor-proteodisco| image:: https://quay.io/repository/biocontainers/bioconductor-proteodisco/status :target: https://quay.io/repository/biocontainers/bioconductor-proteodisco .. _`bioconductor-proteodisco/tags`: https://quay.io/repository/biocontainers/bioconductor-proteodisco?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-proteodisco/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-proteodisco/README.html