recipe bioconductor-cellscore

Tool for Evaluation of Cell Identity from Transcription Profiles

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/CellScore.html

License:

GPL-3

Recipe:

/bioconductor-cellscore/meta.yaml

The CellScore package contains functions to evaluate the cell identity of a test sample, given a cell transition defined with a starting (donor) cell type and a desired target cell type. The evaluation is based upon a scoring system, which uses a set of standard samples of known cell types, as the reference set. The functions have been carried out on a large set of microarray data from one platform (Affymetrix Human Genome U133 Plus 2.0). In principle, the method could be applied to any expression dataset, provided that there are a sufficient number of standard samples and that the data are normalized.

package bioconductor-cellscore

(downloads) docker_bioconductor-cellscore

Versions:
1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0, 

1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

Depends:

  • on bioconductor-biobase >=2.66.0,<2.67.0

  • on bioconductor-summarizedexperiment >=1.36.0,<1.37.0

  • on r-base >=4.4,<4.5.0a0

  • on r-gplots >=3.0.1

  • on r-lsa >=0.73.1

  • on r-rcolorbrewer >=1.1-2

  • on r-squash >=1.0.8

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-cellscore

to add into an existing workspace instead, run:

pixi add bioconductor-cellscore

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-cellscore

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cellscore

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-cellscore:<tag>

(see bioconductor-cellscore/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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