Free and Open-Source Cancer Reporting Tools on GitHub

can you provide list of free available and usually updated software which provide reports for cancer patients like https://github.com/sigven/cpsr and https://github.com/sigven/pcgr and freely available on github?

Certainly! Here are some free and open-source software tools available on GitHub that provide reports for cancer patients, similar to the Cancer Predisposition Sequencing Reporter (CPSR) and the Personal Cancer Genome Reporter (PCGR):

1. cBioPortal for Cancer Genomics

   • GitHub Repository: cBioPortal
   • Description: cBioPortal provides visualization, analysis, and download of large-scale cancer genomics data sets. It is widely used for exploring and analyzing cancer genomics data.

2. OncoKB

   • GitHub Repository: oncokb
   • Description: OncoKB is a precision oncology knowledge base that contains information about the effects and treatment implications of specific cancer gene alterations.

3. CIViC (Clinical Interpretation of Variants in Cancer)

   • GitHub Repository: civic-client
   • Description: CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.

4. OpenCRAVAT

   • GitHub Repository: open-cravat
   • Description: OpenCRAVAT is a scalable, open-source platform for rapidly developing, sharing, and running variant annotation tools.

5. VEP (Variant Effect Predictor)

   • GitHub Repository: ensembl-vep
   • Description: VEP is a tool by Ensembl that predicts the functional effects of genomic variants.

6. Bcbio-nextgen

   • GitHub Repository: bcbio-nextgen
   • Description: Bcbio-nextgen is a toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.

7. Galaxy Project

   • GitHub Repository: galaxy
   • Description: Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.

8. GEMINI (Genetic Epidemiology of Model Organism Informatics)

   • GitHub Repository: gemini
   • Description: GEMINI is a flexible framework for exploring genetic variation in the context of the wealth of existing genome annotations.

9. CIViCpy

   • GitHub Repository: civicpy
   • Description: CIViCpy is a Python client for the CIViC database, which provides programmatic access to the CIViC knowledgebase.

10. Pediatric Cancer Data Commons (PCDC)

    • GitHub Repository: pcdc
    • Description: PCDC provides a platform for sharing and analyzing pediatric cancer data.

These tools are actively maintained and provide various functionalities for analyzing and reporting cancer genomics data. They are freely available on GitHub and can be used to support research and clinical decision-making in