{"repo":"sigven/cpsr","free":true,"listed":false,"github":"https://github.com/sigven/cpsr","clone":"git clone https://github.com/sigven/cpsr.git","description":"Cancer Predisposition Sequencing Reporter (CPSR)","language":"R","stars":65,"topics":["cancer-genomics","inherited","workflow-engine","germline-variants","cancer-research","reporting-tool","report-generator","docker","predisposition","cancer-predisposition"],"license":"MIT","category":"deployment-docker-iac","readme_excerpt":"Cancer Predisposition Sequencing Reporter The Cancer Predisposition Sequencing Reporter (CPSR) is a computational workflow that interprets DNA sequence variants identified from next-generation sequencing in the context of cancer predisposition . CPSR accepts a query file with germline variant calls (SNVs/InDels) from a single sample (i.e. cancer patient), encoded in the VCF format . Through comprehensive gene and variant annotation procedures, CPSR offers the following functionalities to the user: 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 3) Detection of germline biomarkers - for prognosis, diagnosis, or drug sensitivity/resistance in cancer 4) Optional detection and reporting of variants related to adverse events/toxicity for common cancer chemotherapies 5) Optional reporting of secondary/incidental findings (ACMG recommendations) 6) Interactive HTML output report with detailed variant information, gene annotations, and external links to relevant databases The CPSR workflow is integrated with the framework that underlies the Personal Cancer Genome Reporter - PCGR. While PCGR is intended for reporting and analysis of somatic variants detected in a tumor, CPSR is intended for reporting and ranking of germline variants in protein-coding genes that are implicated in cancer predisposition","default_branch":null,"files":null,"tree":[],"storefront":"/r/sigven","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/sigven/cpsr/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}