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/3.18/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:

1.16.0-0,  1.14.1-0,  1.12.0-1,  1.12.0-0,  1.8.0-2,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.2.0-0, 

1.16.0-0,  1.14.1-0,  1.12.0-1,  1.12.0-0,  1.8.0-2,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0a0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0a0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-caret:

>=6.0

depends r-dplyr:

depends r-dynamictreecut:

depends r-fastcluster:

depends r-ggplot2:

>=2.2.1

depends r-glmnet:

>2.0

depends r-locfit:

depends r-rcpp:

depends r-rcpparmadillo:

depends r-rcppparallel:

requirements:

Installation

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-scgps

and update with::

   mamba update bioconductor-scgps

To create a new environment, run:

mamba create --name myenvname bioconductor-scgps

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-scgps:<tag>

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

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Link to this page

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