:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-scgraphverse' .. highlight: bash bioconductor-scgraphverse ========================= .. conda:recipe:: bioconductor-scgraphverse :replaces_section_title: :noindex: scGraphVerse\: A Gene Network Analysis Package :homepage: https://bioconductor.org/packages/3.22/bioc/html/scGraphVerse.html :license: GPL-3 + file LICENSE :recipe: /`bioconductor-scgraphverse `_/`meta.yaml `_ A package for inferring\, comparing\, and visualizing gene networks from single\-cell RNA sequencing data. It integrates multiple methods \(GENIE3\, GRNBoost2\, ZILGM\, PCzinb\, and JRF\) for robust network inference\, supports consensus building across methods or datasets\, and provides tools for evaluating regulatory structure and community similarity. GRNBoost2 requires Python package \'arboreto\' which can be installed using init\_py\(install\_missing \= TRUE\). This package includes adapted functions from ZILGM \(Park et al.\, 2021\)\, JRF \(Petralia et al.\, 2015\)\, and learn2count \(Nguyen et al. 2023\) packages with proper attribution under GPL\-2 license. .. conda:package:: bioconductor-scgraphverse |downloads_bioconductor-scgraphverse| |docker_bioconductor-scgraphverse| :versions: ``1.0.0-0`` :depends on bioconductor-biocbaseutils: ``>=1.12.0,<1.13.0`` :depends on bioconductor-biocbaseutils: ``>=1.12.0,<1.13.0a0`` :depends on bioconductor-biocparallel: ``>=1.44.0,<1.45.0`` :depends on bioconductor-biocparallel: ``>=1.44.0,<1.45.0a0`` :depends on bioconductor-genie3: ``>=1.32.0,<1.33.0`` :depends on bioconductor-genie3: ``>=1.32.0,<1.33.0a0`` :depends on bioconductor-graph: ``>=1.88.0,<1.89.0`` :depends on bioconductor-graph: ``>=1.88.1,<1.89.0a0`` :depends on bioconductor-multiassayexperiment: ``>=1.36.0,<1.37.0`` :depends on bioconductor-multiassayexperiment: ``>=1.36.1,<1.37.0a0`` :depends on bioconductor-s4vectors: ``>=0.48.0,<0.49.0`` :depends on bioconductor-s4vectors: ``>=0.48.0,<0.49.0a0`` :depends on bioconductor-singlecellexperiment: ``>=1.32.0,<1.33.0`` :depends on bioconductor-singlecellexperiment: ``>=1.32.0,<1.33.0a0`` :depends on bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0`` :depends on bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0a0`` :depends on libblas: ``>=3.9.0,<4.0a0`` :depends on libgcc: ``>=14`` :depends on liblapack: ``>=3.9.0,<4.0a0`` :depends on liblzma: ``>=5.8.2,<6.0a0`` :depends on libzlib: ``>=1.3.1,<2.0a0`` :depends on r-base: ``>=4.5,<4.6.0a0`` :depends on r-distributions3: :depends on r-doparallel: :depends on r-dorng: :depends on r-dplyr: :depends on r-glmnet: :depends on r-httr: :depends on r-igraph: :depends on r-jsonlite: :depends on r-mass: :depends on r-matrix: :depends on r-mpath: :depends on r-reticulate: :depends on r-tidyr: :additional platforms: Installation ------------ You need a conda-compatible package manager (currently either `pixi `__, `conda `__, or `micromamba `__) and the Bioconda channel already activated (see :ref:`bioconda_setup`). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda). Pixi """" With pixi_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install globally, run:: pixi global install bioconductor-scgraphverse to add into an existing workspace instead, run:: pixi add bioconductor-scgraphverse In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:: pixi workspace channel add conda-forge pixi workspace channel add bioconda Conda """"" With conda_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install into an existing and activated environment, run:: conda install bioconductor-scgraphverse Alternatively, to install into a new environment, run:: conda create -n envname bioconductor-scgraphverse with ``envname`` being the name of the desired environment. Container """"""""" Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:: docker pull quay.io/biocontainers/bioconductor-scgraphverse: (see `bioconductor-scgraphverse/tags`_ for valid values for ````). Integrated deployment """"""""""""""""""""" Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration. .. _conda: https://conda.io .. _pixi: https://pixi.sh .. |downloads_bioconductor-scgraphverse| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-scgraphverse.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-scgraphverse :alt: (downloads) .. |docker_bioconductor-scgraphverse| image:: https://quay.io/repository/biocontainers/bioconductor-scgraphverse/status :target: https://quay.io/repository/biocontainers/bioconductor-scgraphverse .. _`bioconductor-scgraphverse/tags`: https://quay.io/repository/biocontainers/bioconductor-scgraphverse?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-scgraphverse/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-scgraphverse/README.html