:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-decomptumor2sig' .. highlight: bash bioconductor-decomptumor2sig ============================ .. conda:recipe:: bioconductor-decomptumor2sig :replaces_section_title: :noindex: Decomposition of individual tumors into mutational signatures by signature refitting :homepage: https://bioconductor.org/packages/3.18/bioc/html/decompTumor2Sig.html :license: GPL-2 :recipe: /`bioconductor-decomptumor2sig `_/`meta.yaml `_ Uses quadratic programming for signature refitting\, i.e.\, to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures \(either Alexandrov\-model signatures or Shiraishi\-model signatures\)\, computing weights that reflect the contributions of the signatures to the mutation load of the tumor. .. conda:package:: bioconductor-decomptumor2sig |downloads_bioconductor-decomptumor2sig| |docker_bioconductor-decomptumor2sig| :versions: .. raw:: html
2.18.0-02.16.0-02.14.0-02.10.0-02.8.0-02.6.0-12.6.0-02.4.0-02.2.0-0 ``2.18.0-0``,  ``2.16.0-0``,  ``2.14.0-0``,  ``2.10.0-0``,  ``2.8.0-0``,  ``2.6.0-1``,  ``2.6.0-0``,  ``2.4.0-0``,  ``2.2.0-0``,  ``2.0.0-1`` .. raw:: html
:depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-bsgenome.hsapiens.ucsc.hg19: ``>=1.4.0,<1.5.0`` :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-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene: ``>=3.2.0,<3.3.0`` :depends bioconductor-variantannotation: ``>=1.48.0,<1.49.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-data.table: :depends r-ggplot2: :depends r-ggseqlogo: :depends r-gridextra: :depends r-matrix: :depends r-plyr: :depends r-quadprog: ``>=1.5-5`` :depends r-readxl: :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-decomptumor2sig and update with:: mamba update bioconductor-decomptumor2sig To create a new environment, run:: mamba create --name myenvname bioconductor-decomptumor2sig 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-decomptumor2sig: (see `bioconductor-decomptumor2sig/tags`_ for valid values for ````) .. |downloads_bioconductor-decomptumor2sig| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-decomptumor2sig.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-decomptumor2sig :alt: (downloads) .. |docker_bioconductor-decomptumor2sig| image:: https://quay.io/repository/biocontainers/bioconductor-decomptumor2sig/status :target: https://quay.io/repository/biocontainers/bioconductor-decomptumor2sig .. _`bioconductor-decomptumor2sig/tags`: https://quay.io/repository/biocontainers/bioconductor-decomptumor2sig?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-decomptumor2sig/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-decomptumor2sig/README.html