Dear Wolfgang and Sutirtha, Excellent, thank you for confirming this! There has been a fair amount of back and forth in the development team about whether to push for Bioconductor or not. We’ll proceed with putting it together to submit to Bioconductor.
Best wishes, Greg From: SUTIRTHA CHAKRABORTY <sutirtha_su...@yahoo.co.in> Date: Wednesday, February 22, 2023 at 4:55 AM To: Flanigan, Greg (NIH/NCI) [C] <greg.flani...@nih.gov>, Wolfgang Huber <wolfgang.hu...@embl.org> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: [EXTERNAL] Re: [Bioc-devel] Question on prospective Bioc package Seems like this would be a great contribution. Best Regards Sutirtha On Wednesday, 22 February 2023, 03:02:52 PM IST, Wolfgang Huber <wolfgang.hu...@embl.org> wrote: Dear Greg This sounds like a typical use case for a Bioconductor package. Simplicity is a not a bad thing—robust, well-engineered building blocks that do one thing really well are IMHO often more useful to many than big integrated complex jack of all trades. Thanks and best wishes Wolfgang > Il giorno 17.02.2023, alle ore 18:26, Flanigan, Greg (NIH/NCI) [C] via > Bioc-devel <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> ha > scritto: > > Dear Bioconductor Developer team, > > I�m part of a team at the NCI that is looking at developing a Bioconductor > package, but I want to be sure it is a good fit with the goals of the > Bioconductor project. > > The core of the package is a custom data object that allows users to query > predicted drug performance based on target gene, whether wild-type or mutant, > or to query predicted gene target fitness by drug. The data object is > precomputed based on a variety of sources, and we include methods to modify > the object based on custom data provided by the user. > > If a more detailed dive would help, here is the preprint of the accompanying > paper: > Link<https://www.biorxiv.org/content/biorxiv/early/2022/10/19/2022.10.17.512424.full.pdf<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biorxiv.org%2Fcontent%2Fbiorxiv%2Fearly%2F2022%2F10%2F19%2F2022.10.17.512424.full.pdf&data=05%7C01%7Cgreg.flanigan%40nih.gov%7Cf538f5333b2a4735965f08db14baefee%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638126565468954182%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=i2AM%2B2Xxkthq0T%2BCWsOykhPJHXQjhYemhMR7Yn%2B%2B42U%3D&reserved=0>> > > I think this tool will offer good impact and utility for researchers. Its > predictions are well-validated and it offers a novel method for examining > drug performance on various cancers. However, given the simplicity of this > tool, would it be a good fit for the Bioconductor project? I would appreciate > your opinion. We will be developing it into a package hosted on GitHub either > way. Thank you for your time! > > Sincerely, > Greg > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=05%7C01%7Cgreg.flanigan%40nih.gov%7Cf538f5333b2a4735965f08db14baefee%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638126565468954182%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=cdzRn7odsOPzlOXXH5267fVrV8nZGBDRlrzXG1gw%2BhE%3D&reserved=0> _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=05%7C01%7Cgreg.flanigan%40nih.gov%7Cf538f5333b2a4735965f08db14baefee%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638126565468954182%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=cdzRn7odsOPzlOXXH5267fVrV8nZGBDRlrzXG1gw%2BhE%3D&reserved=0> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
