This repository is part of the family of packages Genomic Analysis of Mature B-cell Lymphomas in R (GAMBLR) developed and maintained by the Morin Lab. This repository contains functionality for molecular/genetic classification of B-cell lymphomas (e.g. BL, FL, and DLBCL). Please refer to the main package for more information.
This package contains the functionality to apply the DLBCLone classifier to identify genetic subgroups of Diffuse Large B-cell Lymphoma (DLBCL) described in the preprint Klossok et al (2025). The repository includes a Shiny interface with some pre-trained models. You can launch this by running GAMBLR.predict:::DLBCLone_shiny(). If you want to classify your own samples using an existing model, the relevant functions to get started are: DLBCLone_load_optimized() and DLBCLone_predict().
This pakage contains functionaliry to apply the random forest classifier to identify genetic subgroups of Follicular Lymphoma cFL/dFL described in Blood (2023). The function that allows to do that is classify_fl(). It either accepts the metadata and mutations in maf format as input data frames to assemble the matrix and perform classification, or it can also accept the matrix prepared in advance. Please refer to the function documentation for the examples and description of supported parameters.
To build the docker image, run the following command in the root of the repository:
docker build -t gamblr.predict .To run the docker image, use the following command:
docker run -it --rm -e PASSWORD='some_password' -p 8787:8787 gamblr.predictThen open your browser and go to http://localhost:8787. You can log in with the username rstudio and the password you set in the command above.