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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
NcountrExperiment.to_anndata()export