:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-aggregatebiovar' .. highlight: bash bioconductor-aggregatebiovar ============================ .. conda:recipe:: bioconductor-aggregatebiovar :replaces_section_title: :noindex: Differential Gene Expression Analysis for Multi\-subject scRNA\-seq :homepage: https://bioconductor.org/packages/3.18/bioc/html/aggregateBioVar.html :license: GPL-3 :recipe: /`bioconductor-aggregatebiovar `_/`meta.yaml `_ For single cell RNA\-seq data collected from more than one subject \(e.g. biological sample or technical replicates\)\, this package contains tools to summarize single cell gene expression profiles at the level of subject. A SingleCellExperiment object is taken as input and converted to a list of SummarizedExperiment objects\, where each list element corresponds to an assigned cell type. The SummarizedExperiment objects contain aggregate gene\-by\-subject count matrices and inter\-subject column metadata for individual subjects that can be processed using downstream bulk RNA\-seq tools. .. conda:package:: bioconductor-aggregatebiovar |downloads_bioconductor-aggregatebiovar| |docker_bioconductor-aggregatebiovar| :versions: ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-3``,  ``1.0.0-2`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-matrix: :depends r-rlang: :depends r-tibble: :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-aggregatebiovar and update with:: mamba update bioconductor-aggregatebiovar To create a new environment, run:: mamba create --name myenvname bioconductor-aggregatebiovar 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-aggregatebiovar: (see `bioconductor-aggregatebiovar/tags`_ for valid values for ````) .. |downloads_bioconductor-aggregatebiovar| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-aggregatebiovar.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-aggregatebiovar :alt: (downloads) .. |docker_bioconductor-aggregatebiovar| image:: https://quay.io/repository/biocontainers/bioconductor-aggregatebiovar/status :target: https://quay.io/repository/biocontainers/bioconductor-aggregatebiovar .. _`bioconductor-aggregatebiovar/tags`: https://quay.io/repository/biocontainers/bioconductor-aggregatebiovar?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-aggregatebiovar/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-aggregatebiovar/README.html