recipe bioconductor-oscope

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

Homepage

https://bioconductor.org/packages/3.11/bioc/html/Oscope.html

License

Artistic-2.0

Recipe

/bioconductor-oscope/meta.yaml

Links

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

Versions

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

Depends

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-ebseq >=1.28.0,<1.29.0

• r-base >=4.0,<4.1.0a0

• r-cluster

• r-testthat

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-oscope

and update with:

conda update bioconductor-oscope

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-oscope:<tag>

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

Link to this page

Render an 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)