:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'somaticseq' .. highlight: bash somaticseq ========== .. conda:recipe:: somaticseq :replaces_section_title: :noindex: An ensemble approach to accurately detect somatic mutations :homepage: https://bioinform.github.io/somaticseq/ :license: BSD / BSD-2-Clause :recipe: /`somaticseq `_/`meta.yaml `_ SomaticSeq is an ensemble caller that has the ability to use machine learning to filter out false positives. The detailed documentation is included in the package\, located in docs\/Manual.pdf. A quick guide can also be found here. SomaticSeq\'s open\-access paper\: Fang LT\, Afshar PT\, Chhibber A\, et al. An ensemble approach to accurately detect somatic mutations using SomaticSeq. Genome Biol. 2015\;16\:197. .. conda:package:: somaticseq |downloads_somaticseq| |docker_somaticseq| :versions: .. raw:: html
3.7.4-03.7.3-03.7.2-03.7.1-03.7.0-03.6.2-03.6.0-03.5.1-03.5.0-0 ``3.7.4-0``,  ``3.7.3-0``,  ``3.7.2-0``,  ``3.7.1-0``,  ``3.7.0-0``,  ``3.6.2-0``,  ``3.6.0-0``,  ``3.5.1-0``,  ``3.5.0-0``,  ``3.4.2-0``,  ``3.4.1-0``,  ``3.4.0-0``,  ``3.3.0-0``,  ``3.2.1-0``,  ``2.8.1-0`` .. raw:: html
:depends bedtools: :depends gatk4: :depends lofreq: :depends muse: :depends numpy: :depends pandas: :depends pysam: :depends python: ``>=3`` :depends r-ada: :depends r-base: :depends scalpel: :depends scipy: :depends vardict: :depends varscan: ``>=2`` :depends xgboost: ``>=1.4`` :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 somaticseq and update with:: mamba update somaticseq To create a new environment, run:: mamba create --name myenvname somaticseq 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/somaticseq: (see `somaticseq/tags`_ for valid values for ````) .. |downloads_somaticseq| image:: https://img.shields.io/conda/dn/bioconda/somaticseq.svg?style=flat :target: https://anaconda.org/bioconda/somaticseq :alt: (downloads) .. |docker_somaticseq| image:: https://quay.io/repository/biocontainers/somaticseq/status :target: https://quay.io/repository/biocontainers/somaticseq .. _`somaticseq/tags`: https://quay.io/repository/biocontainers/somaticseq?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/somaticseq/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/somaticseq/README.html