recipe bioconductor-sipsic

Calculate Pathway Scores for Each Cell in scRNA-Seq Data

Homepage:

https://bioconductor.org/packages/3.20/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:

1.10.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

Depends:

  • on bioconductor-singlecellexperiment >=1.32.0,<1.33.0

  • on r-base >=4.5,<4.6.0a0

  • on r-matrix

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-sipsic

to add into an existing workspace instead, run:

pixi add bioconductor-sipsic

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-sipsic

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-sipsic

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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Render an install-with-bioconda badge with the following MarkDown:

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