:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-desingle' .. highlight: bash bioconductor-desingle ===================== .. conda:recipe:: bioconductor-desingle :replaces_section_title: :noindex: DEsingle for detecting three types of differential expression in single\-cell RNA\-seq data :homepage: https://bioconductor.org/packages/3.18/bioc/html/DEsingle.html :license: GPL-2 :recipe: /`bioconductor-desingle `_/`meta.yaml `_ DEsingle is an R package for differential expression \(DE\) analysis of single\-cell RNA\-seq \(scRNA\-seq\) data. It defines and detects 3 types of differentially expressed genes between two groups of single cells\, with regard to different expression status \(DEs\)\, differential expression abundance \(DEa\)\, and general differential expression \(DEg\). DEsingle employs Zero\-Inflated Negative Binomial model to estimate the proportion of real and dropout zeros and to define and detect the 3 types of DE genes. Results showed that DEsingle outperforms existing methods for scRNA\-seq DE analysis\, and can reveal different types of DE genes that are enriched in different biological functions. .. conda:package:: bioconductor-desingle |downloads_bioconductor-desingle| |docker_bioconductor-desingle| :versions: .. raw:: html
1.22.0-01.20.0-01.18.0-01.14.0-01.12.0-01.10.0-11.10.0-01.8.0-01.6.0-0 ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-1``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.1-0`` .. raw:: html
:depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-bbmle: ``>=1.0.18`` :depends r-gamlss: ``>=4.4-0`` :depends r-mass: ``>=7.3-45`` :depends r-matrix: ``>=1.2-14`` :depends r-maxlik: ``>=1.3-4`` :depends r-pscl: ``>=1.4.9`` :depends r-vgam: ``>=1.0-2`` :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-desingle and update with:: mamba update bioconductor-desingle To create a new environment, run:: mamba create --name myenvname bioconductor-desingle 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-desingle: (see `bioconductor-desingle/tags`_ for valid values for ````) .. |downloads_bioconductor-desingle| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-desingle.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-desingle :alt: (downloads) .. |docker_bioconductor-desingle| image:: https://quay.io/repository/biocontainers/bioconductor-desingle/status :target: https://quay.io/repository/biocontainers/bioconductor-desingle .. _`bioconductor-desingle/tags`: https://quay.io/repository/biocontainers/bioconductor-desingle?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-desingle/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-desingle/README.html