:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-scran' .. highlight: bash bioconductor-scran ================== .. conda:recipe:: bioconductor-scran :replaces_section_title: :noindex: Methods for Single\-Cell RNA\-Seq Data Analysis :homepage: https://bioconductor.org/packages/3.20/bioc/html/scran.html :license: GPL-3 :recipe: /`bioconductor-scran `_/`meta.yaml `_ :links: biotools: :biotools:`scran` Implements miscellaneous functions for interpretation of single\-cell RNA\-seq data. Methods are provided for assignment of cell cycle phase\, detection of highly variable and significantly correlated genes\, identification of marker genes\, and other common tasks in routine single\-cell analysis workflows. .. conda:package:: bioconductor-scran |downloads_bioconductor-scran| |docker_bioconductor-scran| :versions: .. raw:: html
1.34.0-11.34.0-01.30.0-11.30.0-01.28.1-01.26.0-11.26.0-01.22.1-11.22.1-0 ``1.34.0-1``,  ``1.34.0-0``,  ``1.30.0-1``,  ``1.30.0-0``,  ``1.28.1-0``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.22.1-1``,  ``1.22.1-0``,  ``1.22.0-0``,  ``1.20.1-0``,  ``1.18.5-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.1-0``,  ``1.14.0-0``,  ``1.12.1-0``,  ``1.10.1-0``,  ``1.8.4-0``,  ``1.6.2-0``,  ``1.4.5-0`` .. raw:: html
:depends bioconductor-beachmat: ``>=2.22.0,<2.23.0`` :depends bioconductor-beachmat: ``>=2.22.0,<2.23.0a0`` :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0`` :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0a0`` :depends bioconductor-biocparallel: ``>=1.40.0,<1.41.0`` :depends bioconductor-biocparallel: ``>=1.40.0,<1.41.0a0`` :depends bioconductor-biocsingular: ``>=1.22.0,<1.23.0`` :depends bioconductor-biocsingular: ``>=1.22.0,<1.23.0a0`` :depends bioconductor-bluster: ``>=1.16.0,<1.17.0`` :depends bioconductor-bluster: ``>=1.16.0,<1.17.0a0`` :depends bioconductor-delayedarray: ``>=0.32.0,<0.33.0`` :depends bioconductor-delayedarray: ``>=0.32.0,<0.33.0a0`` :depends bioconductor-edger: ``>=4.4.0,<4.5.0`` :depends bioconductor-edger: ``>=4.4.0,<4.5.0a0`` :depends bioconductor-limma: ``>=3.62.0,<3.63.0`` :depends bioconductor-limma: ``>=3.62.1,<3.63.0a0`` :depends bioconductor-matrixgenerics: ``>=1.18.0,<1.19.0`` :depends bioconductor-matrixgenerics: ``>=1.18.0,<1.19.0a0`` :depends bioconductor-metapod: ``>=1.14.0,<1.15.0`` :depends bioconductor-metapod: ``>=1.14.0,<1.15.0a0`` :depends bioconductor-s4arrays: ``>=1.6.0,<1.7.0`` :depends bioconductor-s4arrays: ``>=1.6.0,<1.7.0a0`` :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0`` :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0a0`` :depends bioconductor-scuttle: ``>=1.16.0,<1.17.0`` :depends bioconductor-scuttle: ``>=1.16.0,<1.17.0a0`` :depends bioconductor-singlecellexperiment: ``>=1.28.0,<1.29.0`` :depends bioconductor-singlecellexperiment: ``>=1.28.0,<1.29.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0`` :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc: ``>=13`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends libstdcxx: ``>=13`` :depends r-base: ``>=4.4,<4.5.0a0`` :depends r-bh: :depends r-dqrng: :depends r-igraph: :depends r-matrix: :depends r-rcpp: :depends r-statmod: :requirements: :additional platforms: .. raw:: html linux-aarch64osx-arm64 .. 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-scran and update with:: mamba update bioconductor-scran To create a new environment, run:: mamba create --name myenvname bioconductor-scran 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-scran: (see `bioconductor-scran/tags`_ for valid values for ````) .. |downloads_bioconductor-scran| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-scran.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-scran :alt: (downloads) .. |docker_bioconductor-scran| image:: https://quay.io/repository/biocontainers/bioconductor-scran/status :target: https://quay.io/repository/biocontainers/bioconductor-scran .. _`bioconductor-scran/tags`: https://quay.io/repository/biocontainers/bioconductor-scran?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-scran/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-scran/README.html