recipe bioconductor-sipsic

Calculate Pathway Scores for Each Cell in scRNA-Seq Data

Homepage:

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

License:

file LICENSE

Recipe:

/bioconductor-sipsic/meta.yaml

Infer biological pathway activity of cells from single-cell RNA-sequencing data by calculating a pathway score for each cell (pathway genes are specified by the user). It is recommended to have the data in Transcripts-Per-Million (TPM) or Counts-Per-Million (CPM) units for best results. Scores may change when adding cells to or removing cells off the data. SiPSiC stands for Single Pathway analysis in Single Cells.

package bioconductor-sipsic

(downloads) docker_bioconductor-sipsic

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends r-base:

>=4.3,<4.4.0a0

depends r-matrix:

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-sipsic

and update with::

   mamba update bioconductor-sipsic

To create a new environment, run:

mamba create --name myenvname bioconductor-sipsic

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-sipsic:<tag>

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

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Link to this page

Render an install-with-bioconda 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-sipsic/README.html)