omicverse.io.read_10x_mtx

omicverse.io.read_10x_mtx(path, *, var_names='gene_symbols', make_unique=True, gex_only=True, prefix=None, compressed=True)[source]

Read a 10x Genomics Matrix Market directory.

Parameters:

  • path (str or pathlib.Path) – Directory containing matrix.mtx and matching feature/barcode files.

  • var_names ({'gene_symbols', 'gene_ids'}, default='gene_symbols') – Which feature column should be used as adata.var_names.

  • make_unique (bool, default=True) – Whether to enforce unique var_names when using gene symbols.

  • gex_only (bool, default=True) – If True, keep only features labeled as Gene Expression (v3+ format).

  • prefix (str or None, default=None) – Optional filename prefix before matrix.mtx, features.tsv, and barcodes.tsv.

  • compressed (bool, default=True) – Whether v3+ files are expected to be gzip-compressed (.gz). Set False for plain-text exports such as some STARsolo outputs.

Returns:

Loaded expression matrix with barcodes and feature annotations.

Return type:

anndata.AnnData