flowchart LR
A("GAMBLR.data") --> B("GAMBLR.helpers")
B --> C("GAMBLR.utils")
C --> D("GAMBLR.viz")
D --> E{"Morin Lab member?"}
E -- YES --> F("GAMBLR.results")
E -- NO --> A
GAMBLR family of packages
GAMBLR.data is the first and most basic member of the GAMBLR family of packages. It mostly serves the purpose of storing the bundled data helpful for genomic analysis of B-cell neoplasms in R, but also contains small basic functions serving as API to retrieve this data.
Some of the bundled data is versioned as it is continuously being updated. This includes, but is not limited to, regions targeted by aSHM (new regions are being added as they are identified), the curated list of lymphoma genes, somatic mutation hotspots, etc. Conveniently for the user, unless they request the specific version of the data, the most recent and up-to-date version is used by default.
The GAMBLR family includes:
- GAMBLR.data - this package
- GAMBLR.helpers - a set of low-level functions for data operation
- GAMBLR.utils - higher level set of functions to operate on genomic data
- GAMBLR.viz - set of functions used mostly for visualizations
- GAMBLR.results - used to access the full data in GAMBL project. Only available for members of the Morin Lab and requires access to GSC, but can also be run locally once properly configured and synced.
This diagram illustrates in a simplified way the dependency relationship of different packages in the GAMBLR.family:
All dependencies should be installed automatically for you, just like with any other R package. If not, please report the issue in the appropriate GitHub repo.
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