:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-scddboost' .. highlight: bash bioconductor-scddboost ====================== .. conda:recipe:: bioconductor-scddboost :replaces_section_title: :noindex: A compositional model to assess expression changes from single\-cell rna\-seq data :homepage: https://bioconductor.org/packages/3.18/bioc/html/scDDboost.html :license: GPL (>= 2) :recipe: /`bioconductor-scddboost `_/`meta.yaml `_ scDDboost is an R package to analyze changes in the distribution of single\-cell expression data between two experimental conditions. Compared to other methods that assess differential expression\, scDDboost benefits uniquely from information conveyed by the clustering of cells into cellular subtypes. Through a novel empirical Bayesian formulation it calculates gene\-specific posterior probabilities that the marginal expression distribution is the same \(or different\) between the two conditions. The implementation in scDDboost treats gene\-level expression data within each condition as a mixture of negative binomial distributions. .. conda:package:: bioconductor-scddboost |downloads_bioconductor-scddboost| |docker_bioconductor-scddboost| :versions: ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1``,  ``1.0.0-0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-ebseq: ``>=2.0.0,<2.1.0`` :depends bioconductor-ebseq: ``>=2.0.0,<2.1.0a0`` :depends bioconductor-oscope: ``>=1.32.0,<1.33.0`` :depends bioconductor-oscope: ``>=1.32.0,<1.33.0a0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0a0`` :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-bh: :depends r-cluster: :depends r-ggplot2: :depends r-mclust: :depends r-rcpp: ``>=0.12.11`` :depends r-rcppeigen: ``>=0.3.2.9.0`` :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-scddboost and update with:: mamba update bioconductor-scddboost To create a new environment, run:: mamba create --name myenvname bioconductor-scddboost 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-scddboost: (see `bioconductor-scddboost/tags`_ for valid values for ````) .. |downloads_bioconductor-scddboost| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-scddboost.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-scddboost :alt: (downloads) .. |docker_bioconductor-scddboost| image:: https://quay.io/repository/biocontainers/bioconductor-scddboost/status :target: https://quay.io/repository/biocontainers/bioconductor-scddboost .. _`bioconductor-scddboost/tags`: https://quay.io/repository/biocontainers/bioconductor-scddboost?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-scddboost/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-scddboost/README.html