Why GAMBLR.data?

GAMBLR.data is an open-source portable R library.

If you’ve had issues with importing genomic data from large-scale lymphoma studies, need to work with standardized data used for analysis of somatic variants, find yourself translating between different genome build systems, or just want a great great comprehensive resource of genomic data in B-cell lymphomas, GAMBLR.data is for you.

GAMBLR stands for Genomic Analysis of Mature B-cell Lymphomas in R, and is part of the family of R packages for lymphoma cancer research developed in the Morin Lab at the Simon Fraser University.

GAMBLR family

GAMBLR.data is part of a larger family of R tools for the analysis of lymphoma genomic data.

It is designed to mainly serve as a storage of bundled data resources and works well with other tools in the GAMBLR family. We continue to bundle more data available through this package, as well as improve it’s functionality.

For more details, please refer to the GAMBLR family section.

Local experience

The data bundled with the GAMBLR.data is immediately available upon package installation and does not require internet connection or ssh access to GSC resources. It can run anywhere that R is available without restrictions and limitations.

Use cases

You can use GAMBLR.data at any stage of your lymphoma data analysis workflow.

GAMBLR.data helps with:

  • one-stop shop to obtain somatic variants from BL, DLBCL, and FL cases (studies by Thomas et al, Dreval et al, Schmitz et al, Chapuy et al, Reddy et al.) and variant calls from some DLBCL cell lines.
  • QC metrics from major WGS and WEX studies of B-cell lymphomas (as reported in Dreval et al.)
  • Curated lists of lymphoma genes for all major pathologies
  • Curated list of regions targeted by aSHM in B-cell lymphomas
  • Coordinates of chromosome arms in both genome projections
  • Gene coordinates in both genome projections
  • Coordinates of oncogenes and SV partners in both genome projections
  • Hotspot regions for selected genes in both projections
  • Other resources

For more details, please refer to the bundled data section.

Community

Community discussions primarily happen through issue submission on GitHub.

Getting started

If you’re interested in trying GAMBLR.data we recommend the getting started tutorial.

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