Package Recipe 'r-easydifferentialgenecoexpression'

recipe r-easydifferentialgenecoexpression

A function that reads in the GEO code of a list of probesets or gene symbols, a gene expression dataset GEO accession code, the name of the dataset feature discriminating the two conditions for the differential coexpression, and the values of the two different conditions for the differential coexpression, and returns the significant pairs of genes/probesets with highest differential coexpression (p-value < 0.005). If the input gene list is made of gene symbols, this package associates the probesets to these gene symbols, if found. Platforms available: GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.

Homepage:: https://github.com/davidechicco/easyDifferentialGeneCoexpression
License:: GPL3 / GPL-3.0-only
Recipe:: /r-easydifferentialgenecoexpression/meta.yaml

package r-easydifferentialgenecoexpression¶

Versions:

1.4-1, 1.4-0, 1.0-2, 1.0-1, 1.0-0

Depends:

on bioconductor-annotate
on bioconductor-biobase
on bioconductor-diffcoexp
on bioconductor-geoquery
on bioconductor-limma
on r-base >=4.4,<4.5.0a0
on r-geneexpressionfromgeo
on r-jetset
on r-magrittr
on r-xml2

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 r-easydifferentialgenecoexpression

to add into an existing workspace instead, run:

pixi add r-easydifferentialgenecoexpression

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 r-easydifferentialgenecoexpression

Alternatively, to install into a new environment, run:

conda create -n envname r-easydifferentialgenecoexpression

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/r-easydifferentialgenecoexpression:<tag>

(see r-easydifferentialgenecoexpression/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:

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