recipe bioconductor-getdee2

Programmatic access to the DEE2 RNA expression dataset

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/getDEE2.html

License:

GPL-3

Recipe:

/bioconductor-getdee2/meta.yaml

Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022).

package bioconductor-getdee2

(downloads) docker_bioconductor-getdee2

Versions:

1.20.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.7.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

Depends:

  • on bioconductor-summarizedexperiment >=1.40.0,<1.41.0

  • on r-base >=4.5,<4.6.0a0

  • on r-htm2txt

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-getdee2

to add into an existing workspace instead, run:

pixi add bioconductor-getdee2

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-getdee2

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-getdee2

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-getdee2:<tag>

(see bioconductor-getdee2/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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