https://github.com/edawson/sigan
sigan
https://github.com/edawson/sigan
Last synced: 4 months ago
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sigan
- Host: GitHub
- URL: https://github.com/edawson/sigan
- Owner: edawson
- Created: 2017-08-25T18:09:00.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2019-10-04T13:32:48.000Z (over 5 years ago)
- Last Synced: 2025-01-07T20:47:02.460Z (5 months ago)
- Language: R
- Size: 84 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
sigan
-------
A slightly modified version of the Broad's SignatureAnalyzer tool described in [10.1038/ng.3557](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936490/).
## SignatureAnalyzer
SignatureAnalyzer is a program for detecting somatic mutational signatures.
It uses a Bayesian (Gibbs-sampling) NMF variant. It also provides handling for
hypermutator samples and both L1 and L2 regularization.
The original SignatureAnalyzer code is provided as-is in SignatureAnalyzer.R.
## sigan
sigan is identical to SignatureAnalyzer except:
- it relies on the COSMIC v3 signatures for signature comparison
- It takes an output name for naming samples files.
Certain options are still hardcoded. At some point, it would be useful to make
L1/L2 regularization and hypermutator handling available at the CLI. Right now, these
have to be edited manually in the script.
## Basic sage:
```
Rscript --vanilla ./sigan.R <"STUDY_NAME">
```
## Credit
Jaegil Kim wrote the original SignatureAnalyzer and maintains the copyright.
Eric Dawson modified the code to produce sigan.