recipe bioconductor-oscope

Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq







biotools: oscope, 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.

package bioconductor-oscope

(downloads) docker_bioconductor-oscope



depends bioconductor-biocparallel:


depends bioconductor-ebseq:


depends r-base:


depends r-cluster:

depends r-testthat:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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<tag>

(see `bioconductor-oscope/tags`_ for valid values for ``<tag>``)

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