:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-scbfa' .. highlight: bash bioconductor-scbfa ================== .. conda:recipe:: bioconductor-scbfa :replaces_section_title: :noindex: A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA\-seq :homepage: https://bioconductor.org/packages/3.18/bioc/html/scBFA.html :license: GPL-3 + file LICENSE :recipe: /`bioconductor-scbfa `_/`meta.yaml `_ This package is designed to model gene detection pattern of scRNA\-seq through a binary factor analysis model. This model allows user to pass into a cell level covariate matrix X and gene level covariate matrix Q to account for nuisance variance\(e.g batch effect\)\, and it will output a low dimensional embedding matrix for downstream analysis. .. conda:package:: bioconductor-scbfa |downloads_bioconductor-scbfa| |docker_bioconductor-scbfa| :versions: ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-zinbwave: ``>=1.24.0,<1.25.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-copula: :depends r-ggplot2: :depends r-mass: :depends r-matrix: :depends r-seurat: :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-scbfa and update with:: mamba update bioconductor-scbfa To create a new environment, run:: mamba create --name myenvname bioconductor-scbfa 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-scbfa: (see `bioconductor-scbfa/tags`_ for valid values for ````) .. |downloads_bioconductor-scbfa| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-scbfa.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-scbfa :alt: (downloads) .. |docker_bioconductor-scbfa| image:: https://quay.io/repository/biocontainers/bioconductor-scbfa/status :target: https://quay.io/repository/biocontainers/bioconductor-scbfa .. _`bioconductor-scbfa/tags`: https://quay.io/repository/biocontainers/bioconductor-scbfa?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-scbfa/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-scbfa/README.html