Package Recipe 'bioconductor-aucell'

recipe bioconductor-aucell

AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/AUCell.html
License:: GPL-3
Recipe:: /bioconductor-aucell/meta.yaml

AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules…) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.

package bioconductor-aucell¶

Versions:

1.32.0-0, 1.28.0-0, 1.24.0-0, 1.22.0-0, 1.20.1-0, 1.16.0-0, 1.14.0-0, 1.12.0-1, 1.12.0-0,

1.32.0-0, 1.28.0-0, 1.24.0-0, 1.22.0-0, 1.20.1-0, 1.16.0-0, 1.14.0-0, 1.12.0-1, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.6.1-0, 1.4.1-0, 1.4.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-delayedmatrixstats >=1.32.0,<1.33.0
on bioconductor-gseabase >=1.72.0,<1.73.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-matrix
on r-mixtools
on r-r.utils

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-aucell

to add into an existing workspace instead, run:

pixi add bioconductor-aucell

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-aucell

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-aucell

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-aucell:<tag>

(see bioconductor-aucell/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.

Download stats¶

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-aucell/README.html)