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Molecule Info H5 Helpers
This repository contains a set of helper functions for reading, subsampling and in future versions visualizing the data in the molecule info h5 files as generated by cellranger.
Installation
pip install molecule_info
Usage
Subsampling
import molecule_info as mi
# read
m = mi.MoleculeInfo(path)
# subsample
m.sample_reads(1000, seed=42)
# convert to anndata
adata = m.to_adata()
Select subset of features
import molecule_info as mi
# read
m = mi.MoleculeInfo(path)
# select features (inplace!)
features = ["C0310", "C0311", "C0312"]
m.select_features(features)
# whitelist
barcodes = ["AAACCTGAGGAGTCTG-1", "AAACCTGAGGAGTCTC-1"]
m.select_barcodes(barcodes)
# convert to anndata
adata = m.to_adata()
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