:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'r-shazam' .. highlight: bash r-shazam ======== .. conda:recipe:: r-shazam :replaces_section_title: :noindex: Provides a computational framework for analyzing mutations in immunoglobulin \(Ig\) sequences. Includes methods for Bayesian estimation of antigen\-driven selection pressure\, mutational load quantification\, building of somatic hypermutation \(SHM\) models\, and model\-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations\: Gupta and Vander Heiden\, et al \(2015\) \\, Yaari\, et al \(2012\) \\, Yaari\, et al \(2013\) \\, Cui\, et al \(2016\) \. :homepage: http://shazam.readthedocs.io :license: AGPL / AGPL-3 :recipe: /`r-shazam `_/`meta.yaml `_ .. conda:package:: r-shazam |downloads_r-shazam| |docker_r-shazam| :versions: .. raw:: html
1.1.2-11.1.2-01.1.0-00.2.3-10.2.3-00.2.2-00.2.1-10.2.1-00.1.11-0 ``1.1.2-1``,  ``1.1.2-0``,  ``1.1.0-0``,  ``0.2.3-1``,  ``0.2.3-0``,  ``0.2.2-0``,  ``0.2.1-1``,  ``0.2.1-0``,  ``0.1.11-0``,  ``0.1.10-1``,  ``0.1.10-0``,  ``0.1.9-2`` .. raw:: html
:depends r-alakazam: ``>=1.1.0`` :depends r-ape: :depends r-base: ``>=4.2,<4.3.0a0`` :depends r-diptest: :depends r-doparallel: :depends r-dplyr: ``>=0.8.1`` :depends r-foreach: :depends r-ggplot2: ``>=3.3.4`` :depends r-igraph: :depends r-iterators: :depends r-kedd: :depends r-kernsmooth: :depends r-lazyeval: :depends r-mass: :depends r-progress: :depends r-rlang: :depends r-scales: :depends r-seqinr: :depends r-stringi: ``>=1.1.3`` :depends r-tidyr: :depends r-tidyselect: :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 r-shazam and update with:: mamba update r-shazam To create a new environment, run:: mamba create --name myenvname r-shazam 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/r-shazam: (see `r-shazam/tags`_ for valid values for ````) .. |downloads_r-shazam| image:: https://img.shields.io/conda/dn/bioconda/r-shazam.svg?style=flat :target: https://anaconda.org/bioconda/r-shazam :alt: (downloads) .. |docker_r-shazam| image:: https://quay.io/repository/biocontainers/r-shazam/status :target: https://quay.io/repository/biocontainers/r-shazam .. _`r-shazam/tags`: https://quay.io/repository/biocontainers/r-shazam?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/r-shazam/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/r-shazam/README.html