- recipe bioconductor-hgu133plus2cellscore
CellScore Standard Cell Types Expression Dataset [hgu133plus2]
- Homepage:
https://bioconductor.org/packages/3.20/data/experiment/html/hgu133plus2CellScore.html
- License:
GPL-3
- Recipe:
The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object.
- package bioconductor-hgu133plus2cellscore¶
- Versions:
1.30.0-0,1.26.0-0,1.22.0-0,1.20.0-0,1.18.0-0,1.14.0-1,1.14.0-0,1.12.0-0,1.10.0-1,1.30.0-0,1.26.0-0,1.22.0-0,1.20.0-0,1.18.0-0,1.14.0-1,1.14.0-0,1.12.0-0,1.10.0-1,1.10.0-0,1.8.0-0,1.6.0-0,1.4.0-1,1.2.0-0- Depends:
on bioconductor-biobase
>=2.70.0,<2.71.0on bioconductor-data-packages
>=20260207on curl
on r-base
>=4.5,<4.6.0a0
- 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-hgu133plus2cellscore
to add into an existing workspace instead, run:
pixi add bioconductor-hgu133plus2cellscore
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-hgu133plus2cellscore
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-hgu133plus2cellscore
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-hgu133plus2cellscore:<tag>
(see bioconductor-hgu133plus2cellscore/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:
[](http://bioconda.github.io/recipes/bioconductor-hgu133plus2cellscore/README.html)
