🧬 immunarch is evolving towards 1.0.0: updates feed (latest update: Oct 15, 2025)

[vadimnazarov]

👀 Updates

• Apr 14, 2025 (this message) – notice about the upcoming changes
• Oct 15, 2025 (link) – CRAN release 0.10.3. Available features:
  • single-cell data analysis support and a tutorial on that;
  • general migration information;
  • a how-to on importing data from immunarch 0.9 to immunarch 0.10;
  • multiple how-tos on reading AIRR-C and 10x formats;
  • repertoire-level features such as gene usage, diversity, and clonality: run ?airr_stats, ?airr_public, ?airr_clonality, ?airr_diversity, and ?annotate_clonality for more information;
  • immundata is usable for the majority of use cases – bulk/single-cell/spatial, out-of-memory.

🧬 Immunarch Is Evolving

Hi everyone,

I want to give you an early heads-up that immunarch (currently in the 0.x series) is about to undergo major changes on its journey toward version 1.0.0. While I haven’t officially published these changes yet, I’d like to make sure you’re aware of what’s coming and how you can stay informed as we approach the first major update in Oct 2025. I’ll keep updating this issue and adding news right here as immunarch continues to evolve.

🤔 Why This Matters

• Performance & Usability: we’re planning to make immunarch faster, more user-friendly, and more robust, to handle more complex and larger datasets – single-cell, large-scale, etc.
• Future-Proofing: as immunarch matures, we’ll streamline features to align with the AIRR Community guidelines on file formats, and drop the support for other formats.
• Stability & A Long-Awaited Publication: the upcoming 1.0.0 release will be more stable, introducing new functionality while phasing out some older code that may not be maintained in the long run.

⏱️ When to Expect More Information

• Official Update No. 1: Slated for October 2025 (updated from previous too optimistic expectations). this will detail the exact features moving to separate packages, newly introduced functions, legacy deprecations, and how to migrate your code seamlessly.
• Startup Messages in R: keep an eye on immunarch’s startup message (printed when you load the package). I’ll use that message channel to announce major steps, share links, and help you migrate successfully.
• In-Package News Functions: those functions will be available in the Apr-May release.
  • get_immunarch_news(): retrieves the most recent official update (once posted).
  • list_immunarch_news(): shows all available updates so you can revisit anything you missed.

📧 Additional Ways to Stay Up to Date

• b-t.cr Forum: I’ll post more detailed information and host discussions on the b-t.cr forum.
• AIRR Slack: Join the AIRR Slack community, where I’ll also share bulletins and answer questions in real time.

❓ Questions or Feedback?

If you have any questions, comments, or ideas about these upcoming changes, feel free to:

• Reply here in this GitHub issue
• Post on the b-t.cr thread
• Join the conversation on the AIRR Slack

🥺 Want to Help?

I would greatly appreciate any problem, especially for single-cell or paired chain data, that you don't know how to solve with the current implementation of immunarch. It could help me focus on the most prevalent use cases and implement streamlined workflows specifically for them.

--
Vadim

[korMichi]

Thank you for creating and maintaining immunarch! It is a great tool and I enjoy working with it. I have a question concerning the new update. Will it include functionality to analyse metaclones identified by seqCluster? For example: I would love to track metaclones using trackClonotypes or do basic statistics and clonality analyses using the clusters. I think it might have been mentioned in #433.
Best wishes and looking forward to the update
Michael

[vadimnazarov]

@korMichi Hi Michael, thank you for the kind words, I greatly appreciate it. The short answer: The first pre-release public version will include some levenshtein and hamming-based functionality for tracking / annotating receptors. No receptor graphs / "meta-clones" / "meta-clonotypes" yet, though; however, this is to come as well. But there is an alterantive - to use TCRdist / other packages for creating graphs, and annotating the immunarch dataset with this "external" information. One of the first tutorials I want to publish is precisely on this topic.

Thanks to splitting Immunarch into two packages, one focusing on data analysis and the other "secret" focusing on data management, it made it much easier to implement distance-based computations in the very first public versions – a prime example of why good architecture really matters and why a rewrite was needed.

I'm sorry to keep you waiting (and not delivering the graph-based functionality in the first versions...), but I want to make sure I have the basics of the docs and some first tutorial(s) ready for publishing. Otherwise, people would just be confused, as the rewrite is quite massive.

[vadimnazarov]

To everyone: please feel free to leave a 👍 on messages in this thread which specify use cases to implement, and/or suggest something you require for your use case. This helps me prioritise specific developments or tutorials.

[vadimnazarov]

https://github.com/immunomind/immundata – immundata is up and running. I'm polishing the pre-(pre)-pre-release code and documentation for immunarch with the immundata support. I'm not sure about next week, but I will try to make it ASAP, as there is no option to analyse data using immundata via immunarch functions before I push the new code. In the meantime, if you have time and interest, please feel free to take a look at the immundata link, experiment with it and ask me questions. The strategy is to release early and gather user feedback. Thank you.

[linqy-immune]

Hi@vadimnazarov ,
I am soooo surprised to find that immundata has come to me and it looks so powerful. I started my bioinformatics analysis by immunarch with the help of the website "https://immunarch.com/index.html". This is really helpful. I wonder whether there is something like the website above for immundata so that we can get started quickly? I can't wait to have a try!

[vadimnazarov]

Hi @linqy-immune thank you! Hopefully, I will be able to release a new version of immunarch with the immundata support and a quite long tutorial on how to use immundata with immunarch for paired-chain single-cell analysis over the weekend / early next week. So it's coming, and thank you for your patience. I sincerely appreciate it!

[linqy-immune]

Hello, @vadimnazarov
Long time no see. How I wish to use the newest version immundata now!
But it is a little pity that I find it inaccessible to get to immundata website.

When can we get the instruction docs? Whether is it appropriate to analyze single cell data?

[vadimnazarov]

Hello @linqy-immune thank you for your patience, I sincerely appreciate it. New immundata and (!) immunarch are on their way to CRAN now. I will post in this thread this or next week once they will be available on CRAN.

The documentation for both packages will be available on https://immunomind.github.io/docs/ – for convenience, there is a single website for all current and, hopefully, future ecosystem packages.

[linqy-immune]

Oops, thanks a lot for all of your effort in Immundata and Immunarch. It would be a great contribution to immune repertoire exploration and means a lot to the fans of immunarch like me.
But when I try to read immunomind document, I still find it unavailable to get normal pages and get helpful information through the website you provide above. The website what I see are attached below. Does this mean that there exists some network problem or the website maintenance?

[vadimnazarov]

Hey @linqy-immune, yes, consider this a maintenance update. All will be working correctly after the release, but before that, there could be some missing pages and small issues.