recipe bioconductor-scgps

A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)

Homepage

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

License

GPL-3

Recipe

/bioconductor-scgps/meta.yaml

The package implements two main algorithms to answer two key questions: a SCORE (Stable Clustering at Optimal REsolution) to find subpopulations, followed by scGPS to investigate the relationships between subpopulations.

package bioconductor-scgps

Versions

1.2.0-0,  1.0.0-0

Depends

• bioconductor-deseq >=1.39.0,<1.40.0

• bioconductor-singlecellexperiment >=1.10.0,<1.11.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• libstdcxx-ng >=7.3.0

• r-base >=4.0,<4.1.0a0

• r-caret >=6.0

• r-dplyr

• r-dynamictreecut

• r-fastcluster

• r-ggplot2 >=2.2.1

• r-glmnet >2.0

• r-locfit

• r-rcpp

• r-rcpparmadillo

• r-rcppparallel

Required By

Installation

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

conda install bioconductor-scgps

and update with:

conda update bioconductor-scgps

or use the docker container:

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

(see bioconductor-scgps/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-scgps/README.html)