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singgroup/r-dreimt-scripts

By singgroup

•Updated almost 6 years ago

Docker image with R, libraries, and data files required by the DREIMT application (www.dreimt.org).

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singgroup/r-dreimt-scripts repository overview

⁠DREIMT r-dreimt-scripts Docker image

The DREIMT r-dreimt-scripts Docker image contains:

  • The custom data analysis scripts written in R to perform the signatures comparison and drug association analyses. These scripts are publicly available here: https://gitlab.com/bu_cnio/DREIMT⁠
  • The neccessary input files from the DREIMT database required to run such scripts.

Each image is tagged with the database version used to build it.

⁠Examples

The following examples show how to analyze an input file named signature.gmt or geneset.gmt placed in the current working directory.

⁠Drug association analysis with SIGNATURE input

docker run --rm -it -v $(pwd):$(pwd) singgroup/r-dreimt-scripts:v20200516 Rscript /opt/dreimt/dreimt/src/DrugAssociation/Dreimt_UPDN_tau_UserQuery.R $(pwd)/signature.gmt /opt/dreimt/resources/D1_short_t_matrix_12434_4690_LINCS.rds /opt/dreimt/resources/sig_id_table_LINCS_short.tsv 500 2 /opt/dreimt/resources/DBprecalculated.Coordinated.ES.SIG.rds /opt/dreimt/resources/Normalized_ES_SIG.rds $(pwd)/results-cmap-signature

⁠Drug association analysis with GENESET input

docker run --rm -it -v $(pwd):$(pwd) singgroup/r-dreimt-scripts:v20200516 Rscript /opt/dreimt/dreimt/src/DrugAssociation/Dreimt_UP_tau_UserQuery.R $(pwd)/geneset.gmt /opt/dreimt/resources/D1_short_t_matrix_12434_4690_LINCS.rds /opt/dreimt/resources/sig_id_table_LINCS_short.tsv 500 2 /opt/dreimt/resources/DBprecalculated.Coordinated.ES.GS.rds /opt/dreimt/resources/Normalized_ES_GS.rds $(pwd)/results-cmap-geneset

⁠Similar signatures analysis with SIGNATURE input

docker run --rm -it -v $(pwd):$(pwd) singgroup/r-dreimt-scripts:v20200516 Rscript /opt/dreimt/dreimt/src/SignatureComparison/Hypergeom_Sig.R $(pwd)/signature.gmt /opt/dreimt/resources/D1geneUniverse.rds /opt/dreimt/resources/Dreimt_Genesets_clean.gmt TRUE $(pwd)/results-jaccard-signature

⁠Similar signatures analysis with GENESET input

docker run --rm -it -v $(pwd):$(pwd) singgroup/r-dreimt-scripts:v20200516 Rscript /opt/dreimt/dreimt/src/SignatureComparison/Hypergeom_GS.R $(pwd)/geneset.gmt /opt/dreimt/resources/D1geneUniverse.rds /opt/dreimt/resources/Dreimt_Genesets_clean.gmt TRUE $(pwd)/results-jaccard-geneset

Tag summary

Content type

Image

Digest

Size

2.4 GB

Last updated

almost 6 years ago

docker pull singgroup/r-dreimt-scripts:v20200914