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make links to guidelines
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sigven committed Jul 13, 2024
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4 changes: 2 additions & 2 deletions README.md
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The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual tumor genomes for precision cancer medicine. It interprets primarily somatic SNVs/InDels and copy number aberrations, and has additional support for interpretation of bulk RNA-seq expression data. The software classifies variants both with respect to _oncogenicity_, and _actionability_. Interactive HTML output reports allow the user to interrogate the clinical impact of the molecular findings in an individual tumor.

- Variant classification
- according to *oncogenicity*: evaluating the oncogenic potential of somatic DNA aberrations (VICC/CGC/ClinGen guidelines)
- according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations (AMP/ASCO/CAP guidelines)
- according to *oncogenicity*: evaluating the oncogenic potential of somatic DNA aberrations ([VICC/CGC/ClinGen guidelines](https://pubmed.ncbi.nlm.nih.gov/35101336/))
- according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations ([AMP/ASCO/CAP guidelines](https://pubmed.ncbi.nlm.nih.gov/27993330/))
- Tumor mutational burden (TMB) estimation
- Mutational signature analysis
- Microsatellite instability (MSI) classification
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4 changes: 2 additions & 2 deletions pcgrr/pkgdown/index.md
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The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual tumor genomes for precision cancer medicine. It interprets primarily somatic SNVs/InDels and copy number aberrations, and has additional support for interpretation of bulk RNA-seq expression data. The software classifies variants both with respect to _oncogenicity_, and _actionability_. Interactive HTML output reports allow the user to interrogate the clinical impact of the molecular findings in an individual tumor.

- Variant classification
- according to *oncogenicity*: evaluating the oncogenic potential of somatic DNA aberrations (VICC/CGC/ClinGen guidelines)
- according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations (AMP/ASCO/CAP guidelines)
- according to *oncogenicity*: evaluating the oncogenic potential of somatic DNA aberrations ([VICC/CGC/ClinGen guidelines](https://pubmed.ncbi.nlm.nih.gov/35101336/))
- according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations ([AMP/ASCO/CAP guidelines](https://pubmed.ncbi.nlm.nih.gov/27993330/))
- Tumor mutational burden (TMB) estimation
- Mutational signature analysis
- Microsatellite instability (MSI) classification
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