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updated README
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sigven committed Sep 29, 2024
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Expand Up @@ -6,7 +6,7 @@ The *Cancer Predisposition Sequencing Reporter (CPSR)* is a computational workfl

1) Flexible **selection of cancer predisposition genes** subject to analysis and reporting - through the use of virtual gene panels
2) **Variant classification** (*Pathogenic* to *Benign*) through a dedicated implementation of [ACMG/AMP guidelines](https://pubmed.ncbi.nlm.nih.gov/25741868/)
3) **Detection of germline biomarkers** - for prognosis, diagnosis, or drug sensitivity/resistance
3) **Detection of germline biomarkers** - for prognosis, diagnosis, or drug sensitivity/resistance in cancer
4) Reporting of **secondary/incidental findings** ([ACMG recommendations](https://pubmed.ncbi.nlm.nih.gov/37347242/))
5) **Interactive HTML output report** with detailed variant information, gene annotations, and external links to relevant databases

Expand All @@ -18,6 +18,10 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos

## News

- *September 2024*: **2.1.0 release**
- data bundle upgrade
- re-calibration of classification tresholds
- [CHANGELOG](https://sigven.github.io/cpsr/articles/CHANGELOG.html)
- *August 2024*: **2.0.3 release**
- patch with bug fix for copying in quarto templates ([pr62](https://github.com/sigven/cpsr/pull/62))
- [CHANGELOG](https://sigven.github.io/cpsr/articles/CHANGELOG.html)
Expand All @@ -32,20 +36,11 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
- [CHANGELOG](https://sigven.github.io/cpsr/articles/CHANGELOG.html)
- *November 2022*: **1.0.1 release**
- Added CPSR logo (designed by [Hal Nakken](https://halvetica.net))
- *February 2022*: **1.0.0 release**
- Complete restructure of code and Conda installation routines, contributed largely by the great [\@pdiakumis](https://github.com/pdiakumis)
- Updated data bundle
- ClinVar - Feb 2022
- CancerMine - Dec 2021
- UniprotKB - Nov 2021
- CIViC - Feb 2022
- GWAS catalog - Dec 2021
- Software upgrade (VEP 105, R/BioConductor)
- New documentation site (<https://sigven.github.io/cpsr>)

## Example report

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12734384.svg)](https://doi.org/10.5281/zenodo.12734384)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13855978.svg)](https://doi.org/10.5281/zenodo.13855978)


## Getting started

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