recipe bioconductor-usort

uSORT: A self-refining ordering pipeline for gene selection

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/uSORT.html

License:

Artistic-2.0

Recipe:

/bioconductor-usort/meta.yaml

This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data. It incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization.

package bioconductor-usort

versions:

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0, 

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-monocle:

>=2.30.0,<2.31.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

depends r-fpc:

depends r-gplots:

depends r-igraph:

depends r-matrix:

depends r-plyr:

depends r-rann:

depends r-rspectra:

depends r-vgam:

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-usort

and update with::

   mamba update bioconductor-usort

To create a new environment, run:

mamba create --name myenvname bioconductor-usort

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-usort:<tag>

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

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