Add ncountr

[princello]

Add ncountr to the scverse ecosystem

ncountr is the first Python package for end-to-end Nanostring nCounter gene expression analysis. It provides RCC file parsing, quality control, normalization (positive-control, CodeSet content, and housekeeping), differential expression testing (via DESeq2-style negative binomial GLMs), and gene set scoring.

AnnData integration

ncountr provides a to_anndata() method that exports the full NcountrExperiment (raw/normalized counts, sample metadata, gene annotations, and QC metrics) into an AnnData object, enabling seamless downstream analysis with scanpy and the broader scverse ecosystem.

Checklist

• OSI-approved license: MIT
• Versioned releases: published on PyPI
• CI/CD: GitHub Actions (workflows)
• API documentation: hosted on Read the Docs
• AnnData integration: NcountrExperiment.to_anndata() export

[muskanhashim]

Thanks for the submission! I reviewed the code against our checklist and it's in great shape

We would like to flag, though, that the PR uses a shortened checklist, and it's missing the mandatory item

"I am an author or maintainer of the tool and agree on listing the package on the scverse website"

Could you paste the full checklist from the repo README and tick all mandatory items including this? That author-consent confirmation is required for us to list the package

Two more minor, non-blocking notes: the "automated tests" checklist item is also missing, though your tests clearly cover it; and the version field reads "v0.1.0" while PyPI lists it as "0.1.0". You may want to drop the "v"?

Other feedback (not related to the checklist): currently AnnData only comes in at the end via to_anndata(), while the analysis runs on the NanostringExperiment object. That's completely fine but it would just be nice if a tutorial showed how to take the exported AnnData onward into a scanpy workflow, so users can see how ncountr plugs into the broader scverse ecosystem!

Thanks again!