:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-oscope' .. highlight: bash bioconductor-oscope =================== .. conda:recipe:: bioconductor-oscope :replaces_section_title: :noindex: Oscope \- A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA\-seq :homepage: https://bioconductor.org/packages/3.18/bioc/html/Oscope.html :license: Artistic-2.0 :recipe: /`bioconductor-oscope `_/`meta.yaml `_ :links: biotools: :biotools:`oscope`, doi: :doi:`10.1038/nmeth.3549` Oscope is a statistical pipeline developed to identifying and recovering the base cycle profiles of oscillating genes in an unsynchronized single cell RNA\-seq experiment. The Oscope pipeline includes three modules\: a sine model module to search for candidate oscillator pairs\; a K\-medoids clustering module to cluster candidate oscillators into groups\; and an extended nearest insertion module to recover the base cycle order for each oscillator group. .. conda:package:: bioconductor-oscope |downloads_bioconductor-oscope| |docker_bioconductor-oscope| :versions: .. raw:: html
1.32.0-01.30.0-01.28.0-01.24.0-01.22.0-01.20.0-11.20.0-01.18.0-01.16.0-0 ``1.32.0-0``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.1-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0`` .. raw:: html
:depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-ebseq: ``>=2.0.0,<2.1.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-cluster: :depends r-testthat: :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-oscope and update with:: mamba update bioconductor-oscope To create a new environment, run:: mamba create --name myenvname bioconductor-oscope 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-oscope: (see `bioconductor-oscope/tags`_ for valid values for ````) .. |downloads_bioconductor-oscope| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-oscope.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-oscope :alt: (downloads) .. |docker_bioconductor-oscope| image:: https://quay.io/repository/biocontainers/bioconductor-oscope/status :target: https://quay.io/repository/biocontainers/bioconductor-oscope .. _`bioconductor-oscope/tags`: https://quay.io/repository/biocontainers/bioconductor-oscope?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-oscope/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-oscope/README.html