[Bioc-devel] GitHub repository for Bioconductor submission of OmniCorr

[Kern, Lori]

You can submit your forked version.   In the end, Bioconductor creates a mirror on a Bioconductor location that is different than both of those Github repos.  However you want to keep the Bioconductor location synced is up to you, but that is the location of the code/package version that is distributed to the Bioconductor community.  The url that is used for submission will be the initial version used for the Bioconductor mirror set up and the initial github user id that is given initial push access to the Bioconductor location.



Lori Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Veronica Quarato <vequa7472 using nmbu.no>
Sent: Tuesday, September 15, 2026 9:54 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>; maintainer using bioconductor.org <maintainer using bioconductor.org>
Cc: Torgeir Rhoden Hvidsten <torgeir.r.hvidsten using nmbu.no>; Shashank Gupta <shashank.gupta using oru.se>
Subject: [Bioc-devel] GitHub repository for Bioconductor submission of OmniCorr

To whom it may concern,

My name is Veronica Quarato, PhD candidate at the Norwegian University of Life Sciences (NMBU), Norway.

I am preparing a new package submission to Bioconductor for OmniCorr, an R package for integrating and visualizing multi-omics data.

I have a question about which GitHub repository I should use for the submission. OmniCorr was published in Bioinformatics Advances in February 2026, and the published paper links to the original GitHub repository:

https://secure-web.cisco.com/1X3nN1M5d2DlbAZrzkZQKqKXe2lZkshiv_SWjtq2iXflco06CuPY_S5N5ozxPN_nhqxY8w_WuaW5EN576teybXl4I8gpdqnYlOSqw3ksDfwyb-Wpuy65ycAmvUqrvgJtFH_iVsw2NqVtne9R_7_0f9liIE-1PiXzjV_C3FCEPE-rCeTYjaww_Z6udgJT5CPeg6V60ivYBID71GYvVLvzdYBLZOCyhkBgMLiYL0NRBDFnNLq2R2BUoW0it2Oa6HVWpuxCkVBJxYbNlakvqleeMNFd2gbf-Cq3mPc1ktp6ENNuWqFih3c6_5g8A1ItOJbat/https%3A%2F%2Fgithub.com%2Fshashank-KU%2FOmniCorr

The original repository was created by the co-author Shashank Gupta. He has now added me as a contributor with the cre role, and I will be the Bioconductor maintainer.

I also have a fork of the repository:

https://secure-web.cisco.com/16akq6K_htKq-YA-H2bDH9wZa3q8tw6G8mC8Mgi6O2pWP0W9g4frLuaMYXIHJaOvyj_5YRCpXl1QgmFHqmepLdBlIFlg6xEeZ0pEIxVLMMJFheL6JDDVY8BkWWb0GmLBMnLJqNZhWYFK0yLFIvyPWeAxn8ciqPmGWzh9A9r113h8MnbA54xnNO3PtO9vhJMaGvY-exndzX2jsMUo7zPmRaakM8C-Igsz9fKPpojRchn-yKJO4P2f18j7FStdCvQkNqEf8F9F2cuzI60FiAqINmuqG75P5sIfqta12mwzhbdK726jfETBqn78Oz-_ARZhK/https%3A%2F%2Fgithub.com%2Fveronicaquarato%2FOmniCorr

My concern is that, during the Bioconductor review process, I may need to make changes to the package in response to reviewer comments. I would prefer not to make those ongoing review changes directly in the GitHub repository linked in the published paper, as the repository represents the version of the software associated with the publication.

Would it be acceptable to submit my fork (veronicaquarato/OmniCorr) to Bioconductor and use it as the development repository during the review process, while keeping the original repository (shashank-KU/OmniCorr) associated with the published paper? After the package is accepted, we could then synchronize the final version with the original repository.

Alternatively, should the original repository be submitted directly to Bioconductor despite this concern?

I would appreciate your advice on the preferred workflow for this situation.

Best regards,

Veronica Quarato
PhD student in Bioinformatics
Norwegian University of Life Sciences

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