:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-celda' .. highlight: bash bioconductor-celda ================== .. conda:recipe:: bioconductor-celda :replaces_section_title: :noindex: CEllular Latent Dirichlet Allocation :homepage: https://bioconductor.org/packages/3.18/bioc/html/celda.html :license: MIT + file LICENSE :recipe: /`bioconductor-celda `_/`meta.yaml `_ Celda is a suite of Bayesian hierarchical models for clustering single\-cell RNA\-sequencing \(scRNA\-seq\) data. It is able to perform \"bi\-clustering\" and simultaneously cluster genes into gene modules and cells into cell subpopulations. It also contains DecontX\, a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. A variety of scRNA\-seq data visualization functions is also included. .. conda:package:: bioconductor-celda |downloads_bioconductor-celda| |docker_bioconductor-celda| :versions: .. raw:: html
1.18.1-01.16.1-01.14.0-11.14.0-01.10.0-21.10.0-11.10.0-01.8.1-01.6.1-1 ``1.18.1-0``,  ``1.16.1-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.10.0-2``,  ``1.10.0-1``,  ``1.10.0-0``,  ``1.8.1-0``,  ``1.6.1-1``,  ``1.6.1-0``,  ``1.4.5-0``,  ``1.2.0-0``,  ``1.0.4-0`` .. raw:: html
:depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0`` :depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0a0`` :depends bioconductor-delayedarray: ``>=0.28.0,<0.29.0`` :depends bioconductor-delayedarray: ``>=0.28.0,<0.29.0a0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0`` :depends bioconductor-scater: ``>=1.30.0,<1.31.0`` :depends bioconductor-scater: ``>=1.30.1,<1.31.0a0`` :depends bioconductor-scran: ``>=1.30.0,<1.31.0`` :depends bioconductor-scran: ``>=1.30.0,<1.31.0a0`` :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-circlize: :depends r-data.table: :depends r-dbscan: :depends r-digest: :depends r-doparallel: :depends r-enrichr: :depends r-foreach: :depends r-ggplot2: :depends r-ggrepel: :depends r-gridextra: :depends r-gtable: :depends r-matrix: :depends r-matrixstats: :depends r-mcmcprecision: :depends r-plyr: :depends r-rcolorbrewer: :depends r-rcpp: :depends r-rcppeigen: :depends r-reshape2: :depends r-rtsne: :depends r-scales: :depends r-stringr: :depends r-uwot: :depends r-withr: :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-celda and update with:: mamba update bioconductor-celda To create a new environment, run:: mamba create --name myenvname bioconductor-celda 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-celda: (see `bioconductor-celda/tags`_ for valid values for ````) .. |downloads_bioconductor-celda| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-celda.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-celda :alt: (downloads) .. |docker_bioconductor-celda| image:: https://quay.io/repository/biocontainers/bioconductor-celda/status :target: https://quay.io/repository/biocontainers/bioconductor-celda .. _`bioconductor-celda/tags`: https://quay.io/repository/biocontainers/bioconductor-celda?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-celda/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-celda/README.html