:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-slalom' .. highlight: bash bioconductor-slalom =================== .. conda:recipe:: bioconductor-slalom :replaces_section_title: :noindex: Factorial Latent Variable Modeling of Single\-Cell RNA\-Seq Data :homepage: https://bioconductor.org/packages/3.18/bioc/html/slalom.html :license: GPL-2 :recipe: /`bioconductor-slalom `_/`meta.yaml `_ slalom is a scalable modelling framework for single\-cell RNA\-seq data that uses gene set annotations to dissect single\-cell transcriptome heterogeneity\, thereby allowing to identify biological drivers of cell\-to\-cell variability and model confounding factors. The method uses Bayesian factor analysis with a latent variable model to identify active pathways \(selected by the user\, e.g. KEGG pathways\) that explain variation in a single\-cell RNA\-seq dataset. This an R\/C\+\+ implementation of the f\-scLVM Python package. See the publication describing the method at https\:\/\/doi.org\/10.1186\/s13059\-017\-1334\-8. .. conda:package:: bioconductor-slalom |downloads_bioconductor-slalom| |docker_bioconductor-slalom| :versions: .. raw:: html
1.24.0-01.22.0-01.20.0-11.20.0-01.16.0-21.16.0-11.16.0-01.14.0-01.12.0-1 ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.16.0-2``,  ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.4.1-0``,  ``1.4.0-0`` .. raw:: html
:depends bioconductor-gseabase: ``>=1.64.0,<1.65.0`` :depends bioconductor-gseabase: ``>=1.64.0,<1.65.0a0`` :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-ggplot2: :depends r-rcpp: ``>=0.12.8`` :depends r-rcpparmadillo: :depends r-rsvd: :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-slalom and update with:: mamba update bioconductor-slalom To create a new environment, run:: mamba create --name myenvname bioconductor-slalom 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-slalom: (see `bioconductor-slalom/tags`_ for valid values for ````) .. |downloads_bioconductor-slalom| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-slalom.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-slalom :alt: (downloads) .. |docker_bioconductor-slalom| image:: https://quay.io/repository/biocontainers/bioconductor-slalom/status :target: https://quay.io/repository/biocontainers/bioconductor-slalom .. _`bioconductor-slalom/tags`: https://quay.io/repository/biocontainers/bioconductor-slalom?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-slalom/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-slalom/README.html