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pegi3s/r_sva

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By i3S

Updated 2 months ago

SVA (https://www.bioconductor.org/packages/release/bioc/html/sva.htm) docker image.

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This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles)

(Please note that the original software licenses still apply)

This image allows the usage of the SVA Bioconductor package, a package that contains several functions for removing batch effects and other unwanted variation in high-throughput experiment

The image includes, among others, the following packages:

Using the r_sva image in Linux

You should adapt and run the following command: docker run --rm -it -v /your/data/dir:/data pegi3s/r_sva Rscript /data/script.R

In this command, you should replace:

  • /your/data/dir to point to the directory that contains the input files you want to analyze and the R script to be executed.
  • script.R to the actual name of your script using sva (i.e. containing library("sva")).

Using the r_sva image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -it -v "/c/Users/User_name/dir/":/data pegi3s/r_sva Rscript /data/script.R

Docker Pull Command

docker pull pegi3s/r_sva