:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-tbsignatureprofiler' .. highlight: bash bioconductor-tbsignatureprofiler ================================ .. conda:recipe:: bioconductor-tbsignatureprofiler :replaces_section_title: :noindex: Profile RNA\-Seq Data Using TB Pathway Signatures :homepage: https://bioconductor.org/packages/3.18/bioc/html/TBSignatureProfiler.html :license: MIT + file LICENSE :recipe: /`bioconductor-tbsignatureprofiler `_/`meta.yaml `_ Gene signatures of TB progression\, TB disease\, and other TB disease states have been validated and published previously. This package aggregates known signatures and provides computational tools to enlist their usage on other datasets. The TBSignatureProfiler makes it easy to profile RNA\-Seq data using these signatures and includes common signature profiling tools including ASSIGN\, GSVA\, and ssGSEA. Original models for some gene signatures are also available. A shiny app provides some functionality alongside for detailed command line accessibility. .. conda:package:: bioconductor-tbsignatureprofiler |downloads_bioconductor-tbsignatureprofiler| |docker_bioconductor-tbsignatureprofiler| :versions: ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.6.0-0``,  ``1.2.0-1``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-assign: ``>=1.38.0,<1.39.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0`` :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0`` :depends bioconductor-edger: ``>=4.0.0,<4.1.0`` :depends bioconductor-gsva: ``>=1.50.0,<1.51.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-singscore: ``>=1.22.0,<1.23.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-dt: :depends r-gdata: :depends r-ggplot2: :depends r-magrittr: :depends r-rcolorbrewer: :depends r-reshape2: :depends r-rlang: :depends r-rocit: :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-tbsignatureprofiler and update with:: mamba update bioconductor-tbsignatureprofiler To create a new environment, run:: mamba create --name myenvname bioconductor-tbsignatureprofiler 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-tbsignatureprofiler: (see `bioconductor-tbsignatureprofiler/tags`_ for valid values for ````) .. |downloads_bioconductor-tbsignatureprofiler| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-tbsignatureprofiler.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-tbsignatureprofiler :alt: (downloads) .. |docker_bioconductor-tbsignatureprofiler| image:: https://quay.io/repository/biocontainers/bioconductor-tbsignatureprofiler/status :target: https://quay.io/repository/biocontainers/bioconductor-tbsignatureprofiler .. _`bioconductor-tbsignatureprofiler/tags`: https://quay.io/repository/biocontainers/bioconductor-tbsignatureprofiler?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-tbsignatureprofiler/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-tbsignatureprofiler/README.html