risserlin/workshop_base_image repository overview

⁠bioc3_19_R4_4

It is a base image built from bioc 3.19 ⁠, and R v4.4. For more info on bioconductor dockers see here⁠ or bioc 3.19 release notes⁠,

and we added the set of packages:

• knitr
• rmarkdown
• httr
• RColorBrewer
• ggplot2,
• kableExtra,
• limma,
• edgeR,
• ComplexHeatmap,
• devtools,
• GEOquery ,
• GEOmetadb,
• BiocGenerics
• biomaRt
• GSEABase
• GSVA
• BiocStyle
• BiocParallel
• seurat
• xaringan
• bookdown
• gprofiler2
• GSA
• RCy3
• fgsea

To run this image run the following:

docker run -v "$(pwd)":/home/rstudio/projects -e PASSWORD=password -p 8787:8787 
--add-host "localhost:###.###.###.###" risserlin/workshop_base_image:bioc3_19_R4_4

• Update the localhost to map to your current IP address.

• map your current working directory to the docker. (If you are using the cytoscpae workflow examples use "$(pwd)"/Cytoscape_workflows as the base directory).

• Once the container is running, in your web browser, go to localhost:8787 and login with the username=rstudio , password=password

⁠bioc3_16_R4_2

It is a base image built from bioc 3.16 ⁠, and R v4.2. For more info on bioconductor dockers see here⁠ or bioc 3.16 release notes⁠,

and we added the set of packages:

• knitr
• rmarkdown
• httr
• RColorBrewer
• ggplot2,
• kableExtra,
• limma,
• edgeR,
• ComplexHeatmap,
• devtools,
• GEOquery ,
• GEOmetadb,
• BiocGenerics
• biomaRt
• GSEABase
• GSVA
• BiocStyle
• BiocParallel
• seurat
• xaringan
• bookdown
• gprofiler2
• GSA
• RCy3
• fgsea

To run this image run the following:

docker run -v "$(pwd)":/home/rstudio/projects -e PASSWORD=password -p 8787:8787 
--add-host "localhost:###.###.###.###" risserlin/workshop_base_image:bioc3_16_R4_2

• Update the localhost to map to your current IP address.

• map your current working directory to the docker. (If you are using the cytoscpae workflow examples use "$(pwd)"/Cytoscape_workflows as the base directory).

• Once the container is running, in your web browser, go to localhost:8787 and login with the username=rstudio , password=password