blcdsdockerregistry/sigprofiler repository overview

⁠docker-SigProfilerExtractor

Repository for the Signature Profiler Extractor tool Dockerfile.

⁠Documentation

Github code: AlexandrovLab/SigProfilerExtractor⁠

SigProfilerExtractor Wiki⁠

⁠Command Usage

see our wiki⁠

general help:
python -m fire SigProfilerExtractor.sigpro

sigProfilerExtractor help:
python -m fire SigProfilerExtractor.sigpro sigProfilerExtractor --help

note: use . instead of import

eg.)
SigProfilerExtractor
  from SigProfilerExtractor (folder in 'python/ dist-packages'
sigpro
  import sigpro (python script 'sigpro.py')
sigProfilerExtractor
   command

⁠Version

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⁠References

⁠Publications:

1. Islam, S M Ashiqul, et al. Uncovering Novel Mutational Signatures by De Novo Extraction with Sigprofilerextractor. (2022) bioRxiv 2020.12.13.422570; doi: https://doi.org/10.1101/2020.12.13.422570⁠ (preprint)

2. Alexandrov, L.B., Kim, J., Haradhvala, N.J. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020). https://doi.org/10.1038/s41586-020-1943-3⁠

3. Omichessan, H., Severi, G., & Perduca, V. (2019). Computational tools to detect signatures of mutational processes in DNA from tumours: A review and empirical comparison of performance. PloS one, 14(9), e0221235. https://doi.org/10.1371/journal.pone.0221235⁠