Quick Start

Full pipeline from config

Create a YAML config file and run the full pipeline:

ncountr init > my_analysis.yaml
# edit my_analysis.yaml with your settings
ncountr run my_analysis.yaml

Python API

import ncountr

# Parse RCC files
exp = ncountr.read_rcc("path/to/rcc_files/")
print(exp)  # NanostringExperiment(785 genes x 47 samples, ...)

# QC
qc_results = ncountr.qc(exp)

# Normalize
ncountr.normalize(exp, method="pos_hk")

# Differential expression
de_results = ncountr.de(exp, group_a=["S1", "S2"], group_b=["S3", "S4"])

# Export to AnnData (for scverse ecosystem)
adata = ncountr.to_anndata(exp)

Download data from GEO

ncountr fetch-geo GSE275334 -o data/

Or from Python:

from ncountr.io.geo import fetch_geo
rcc_dir = fetch_geo("GSE275334", output_dir="data/")