Presubmission Inquiry for gentropy

[project-defiant]

Submitting Author: Name (@github_handle)
Package Name: gentropy One-Line Description of Package: Open Targets python framework for post-GWAS analysis Repository Link (if existing): https://github.com/opentargets/gentropy

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Code of Conduct & Commitment to Maintain Package

• [x] I agree to abide by pyOpenSci's Code of Conduct during the review process and in maintaining my package after should it be accepted.
• [x] I have read and will commit to package maintenance after the review as per the pyOpenSci Policies Guidelines.

Description

Open Targets Gentropy is a Python package to facilitate the interpretation and analysis of GWAS and functional genomic studies for target identification. This package contains a toolkit for the harmonisation, statistical analysis and prioritisation of genetic signals to assist drug discovery.

Community Partnerships

We partner with communities to support peer review with an additional layer of checks that satisfy community requirements. If your package fits into an existing community please check below:

• [ ] Astropy:My package adheres to Astropy community standards
• [ ] Pangeo: My package adheres to the Pangeo standards listed in the pyOpenSci peer review guidebook

Scope

• Please indicate which category or categories this package falls under: Data processing and munging

  Scope

• Please indicate which category or categories. Check out our package scope page to learn more about our scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry):

  • [x] Data retrieval
  • [x] Data extraction
  • [x] Data processing/munging
  • [ ] Data deposition
  • [ ] Data validation and testing
  • [ ] Data visualization
  • [ ] Workflow automation
  • [ ] Citation management and bibliometrics
  • [x] Scientific software wrappers
  • [ ] Database interoperability

Domain Specific

• [ ] Geospatial
• [x] Education

Community Partnerships

If your package is associated with an existing community please check below:

• [ ] Astropy:My package adheres to Astropy community standards

• [ ] Pangeo: My package adheres to the Pangeo standards listed in the pyOpenSci peer review guidebook

• Explain how and why the package falls under these categories (briefly, 1-2 sentences). Please note any areas you are unsure of: Gentropy package allows for retrieval of GWAS genomics data with provided airflow automation from locations like GWAS catalog, GnomAD, Finngen, etc. Whole list of available datasets is present in the datasources

Gentropy also allows for data extraction and processing, as main functionality - step functions provided in the steps allow for conducting Genome wide association studies analysis (GWAS).

Gentropy wraps methods from R coloc package, CARMA and others - each of concrete methods

• Who is the target audience and what are the scientific applications of this package?
  Target audience are scientists, labs and biotech industry companies, who want to perform GWAS analysis themselves.

• Are there other Python packages that accomplish similar things? If so, how does yours differ? vcf2gwas - this is the workflow for the typical GWAS analysis pandasgwas - this is the package to retrieve GWAS data from GWAS catalog

possibly others minor packages and tools for specific GWAS steps

• Any other questions or issues we should be aware of: This is the project maintained by Open Targets

P.S. Have feedback/comments about our review process? Leave a comment here

[Batalex]

Hello @project-defiant, welcome to pyOpenSci! Sorry it took me so long to get back to you. gentropy is definitely in scope for us, would you mind opening a new submission issue referencing this presubmission enquiry? Thank you.

[cmarmo]

Hello @project-defiant: I'm going to close this presubmission to avoid rechecks from the Editors in Chief. Feel free to open your submission issue for gentropy when ready! Thanks!