CRAN task view proposal: Omics

[julieaubert]

Scope: In this task view, we propose to focus on the most important CRAN packages dedicated to genomics data, which have been published more than one year ago and are regularly updated. A few additional packages from Bioconductor are included, not looking for an exhaustive description but pointing to the must-see packages or to packages focused on omics not well covered by CRAN packages. We propose the following structure

• Annotation and Databases
• Genomics
• Transcriptomics
• Proteomics
• Metabolomics
• Other omics
• Multiple omics
• Specific tasks
• Specific application fields

• Packages: We include packages, such as biomartr, WebGestaltR, GenomicTools.fileHandler, Seurat, pagoda2, ChemoSpec, wrProteo, aLFQ, o2plsda, PMA, WGCNA, GeneNet. Our proposal is available in the following github repo

Overlap: The first idea was to create a task view on "Genetics and Genomics", but this ctv seems to be too wide and we decided to split it in two parts : Omics corresponding to this proposal and Genetics which needs to find its maintainer. Complementary information might also be found in r view("Phylogenetics"), r view("MachineLearning"), r view("Agriculture") or r view("MissingData") task views for some specific tasks or specific applications. Maintainers: Julie Aubert, Toby Dylan Hocking, Nathalie Vialaneix

[jpiaskowski]

Hello, as one of the maintainers of the Agriculture task view, I don't see any overlap with ours because we only include applied statistical genetics packages.

I'm not on the CRAN task view committee, but as a user, it would be helpful if the scope was more clearly delineated. The title is "omics" and the sub-headings fit that, but the scope indicates only "genomics".

[julieaubert]

Hello Julia, thanks you for your advice. I will replaced in the text genomics with omics less restrictive and will modify the scope with "The term omics concern various biological disciplines ending with the suffix -omics, such as genomics, proteomics, metabolomics, transcriptomics. In this task view, we focus on the most important CRAN packages dedicated to omics data analysis, ..."

[zeileis]

Julie @julieaubert et al., thank you for this very welcome and thorough task view proposal! Apologies for the late response, I didn't get round earlier to have a closer look.

By and large, I think this is almost ready to go. I just have a couple of comments in the same vein as Julia @jpiaskowski concerning the title and scope:

• Expand topic in header, possibly to: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics
• I think it's a bit weird if the first intro paragraph starts with a description of Bioconductor. Instead, I would rearrange the paragraph a bit: start with explaining the "omics" title, the CRAN focus, and then the relationship to Bioconductor.
• There is a bit of explanation of the scope of the task view but a few more details on which packages should go in or stay out might be useful.
• Do not refer to the task view as "the Genomics task view". I guess that "this task view" would be easier to understand or "Omics task view" if you want to use the official title.

Additionally, I noticed a few formatting details:

• Some bullet points like Cell trajectories: or Protein structure and sequence: seem to end in a backslash that is not necessary.
• The "MaxQuant" link does not seem correctly formatted with some hanging parentheses.
• The bullet point single-cell protein data (CITE-seq): should start with a capital S.
• Is the hyphen in "High dimensional data - regularization" necessary? I would probably just omit it.

If you address these, I think that the task view is ready for release.

[zeileis]

To officially move forward, we need the endorsement of three task view editors. I'm in favor, anyone else: @davidjohannesmeyer @eddelbuettel @rociojoo @rsbivand ? A "thumbs up" for this comment would be sufficient or you can comment below. (I have excluded @tuxette from the list above because I think she would prefer not to have to vote on her own co-proposal.)

[tuxette]

@zeileis : I confirm that I don't want to have to vote ;) And thank you for the feedback!

[julieaubert]

Achim @zeileis thank you for your careful feedback and suggestions. We addressed them and in particular have rewritten the introduction which now seems better suited.

[willgearty]

Glad to see an -omics task view finally come together! I'm the lead maintainer of the Phylogenetics task view, so please let me know how we can help better connect the two task views! From a brief glance at the proposal, I see little if any package overlap between the two task views. At the very least, we'd be more than happy to link to the -omics task view in the Phylogenetics task view.

[zeileis]

Thanks for the update, Julie @julieaubert, this looks good to me and I think we should officially publish the task view now. David @davidjohannesmeyer, Dirk @eddelbuettel, Rocío @rociojoo, Roger @rsbivand, does this have your support? Again, a thumbs up is sufficient.

[tuxette]

Thanks @willgearty ! I don't think that there is overlap with the phylogenetics TV: we have been careful not to include packages related to phylogenetics. I might send you a list of packages that we have excluded and related to phylogenetics if you want to take a look at it. We are linking the phylogenetics TV in our TV so this would be great (and make sense), were you to do the reverse. Thanks again: your feedback is appreciated!

[zeileis]

OK, thanks everyone, we have a sufficient number of endorsements now so that we can officially move towards releasing the task view on CRAN.

Julie @julieaubert could you please transfer ownership of the repository to me personally ("zeileis") and I will then transfer ownership to the "cran-task-views" organization and make you co-admin. And then we can work through resolving the last fine details before we release on CRAN.

For transfer of the ownership, I hope the following should work for you:

Settings > Collaborators > Public Repository / Mange > Danger Zone / Transfer ownership

[zeileis]

Thanks for the transfer! I now set everything up at: https://github.com/cran-task-views/Omics I completed the meta-information, added a README, and did a few small touch-ups (see logs). You are the "Admin" for this repository, Toby is a "Maintainer", and Nathalie is by definition an "Admin" like all of the CRAN Task View Editors. Please have another look at the repository. If you agree that everything is ready, I will do the CRAN release.

[julieaubert]

Thanks @zeileis. I corrected a remaining typo. Everything looks good for me. Let's go

[zeileis]

Great, thank you. I waited with the release until Monday so that the announcement reaches a wider audience.

Task view: https://CRAN.R-project.org/view=Omics Twitter: https://twitter.com/AchimZeileis/status/1642810166050693120 Mastodon: https://fosstodon.org/@zeileis/110134033783285141

Will @willgearty, now you could add a r view("Omics") reference to your task view, that would be great!

[zeileis]

Oh, and I forgot to say: Thank you, Julie @julieaubert, Toby @tdhock, and Nathalie @tuxette, for putting this togeter. It's great to see this finally on CRAN. 🚀

[willgearty]

I've added a reference to the new Omics task view in the Phylogenetics task view!

[zeileis]

Excellent, thanks! I've updated CRAN correspondingly. (Note: Before, I just changed the version/date to use a two-digit month and day.)