:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-signaturesearch' .. highlight: bash bioconductor-signaturesearch ============================ .. conda:recipe:: bioconductor-signaturesearch :replaces_section_title: :noindex: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis :homepage: https://bioconductor.org/packages/3.18/bioc/html/signatureSearch.html :license: Artistic-2.0 :recipe: /`bioconductor-signaturesearch `_/`meta.yaml `_ This package implements algorithms and data structures for performing gene expression signature \(GES\) searches\, and subsequently interpreting the results functionally with specialized enrichment methods. .. conda:package:: bioconductor-signaturesearch |downloads_bioconductor-signaturesearch| |docker_bioconductor-signaturesearch| :versions: .. raw:: html
1.16.0-01.14.0-01.12.0-11.12.0-01.8.2-11.8.2-01.8.0-01.6.1-01.4.3-0 ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.8.2-1``,  ``1.8.2-0``,  ``1.8.0-0``,  ``1.6.1-0``,  ``1.4.3-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-0`` .. raw:: html
:depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0`` :depends bioconductor-annotationdbi: ``>=1.64.1,<1.65.0a0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-clusterprofiler: ``>=4.10.0,<4.11.0`` :depends bioconductor-clusterprofiler: ``>=4.10.0,<4.11.0a0`` :depends bioconductor-delayedarray: ``>=0.28.0,<0.29.0`` :depends bioconductor-delayedarray: ``>=0.28.0,<0.29.0a0`` :depends bioconductor-dose: ``>=3.28.0,<3.29.0`` :depends bioconductor-dose: ``>=3.28.1,<3.29.0a0`` :depends bioconductor-experimenthub: ``>=2.10.0,<2.11.0`` :depends bioconductor-experimenthub: ``>=2.10.0,<2.11.0a0`` :depends bioconductor-fgsea: ``>=1.28.0,<1.29.0`` :depends bioconductor-fgsea: ``>=1.28.0,<1.29.0a0`` :depends bioconductor-gseabase: ``>=1.64.0,<1.65.0`` :depends bioconductor-gseabase: ``>=1.64.0,<1.65.0a0`` :depends bioconductor-hdf5array: ``>=1.30.0,<1.31.0`` :depends bioconductor-hdf5array: ``>=1.30.0,<1.31.0a0`` :depends bioconductor-org.hs.eg.db: ``>=3.18.0,<3.19.0`` :depends bioconductor-org.hs.eg.db: ``>=3.18.0,<3.19.0a0`` :depends bioconductor-qvalue: ``>=2.34.0,<2.35.0`` :depends bioconductor-qvalue: ``>=2.34.0,<2.35.0a0`` :depends bioconductor-reactome.db: ``>=1.86.0,<1.87.0`` :depends bioconductor-reactome.db: ``>=1.86.2,<1.87.0a0`` :depends bioconductor-rhdf5: ``>=2.46.0,<2.47.0`` :depends bioconductor-rhdf5: ``>=2.46.1,<2.47.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends libstdcxx-ng: ``>=12`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-data.table: :depends r-dplyr: :depends r-fastmatch: :depends r-ggplot2: :depends r-magrittr: :depends r-matrix: :depends r-rcpp: :depends r-readr: :depends r-reshape2: :depends r-rsqlite: :depends r-scales: :depends r-tibble: :depends r-visnetwork: :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-signaturesearch and update with:: mamba update bioconductor-signaturesearch To create a new environment, run:: mamba create --name myenvname bioconductor-signaturesearch 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-signaturesearch: (see `bioconductor-signaturesearch/tags`_ for valid values for ````) .. |downloads_bioconductor-signaturesearch| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-signaturesearch.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-signaturesearch :alt: (downloads) .. |docker_bioconductor-signaturesearch| image:: https://quay.io/repository/biocontainers/bioconductor-signaturesearch/status :target: https://quay.io/repository/biocontainers/bioconductor-signaturesearch .. _`bioconductor-signaturesearch/tags`: https://quay.io/repository/biocontainers/bioconductor-signaturesearch?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-signaturesearch/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-signaturesearch/README.html