singlecellexperiment.io package

Submodules

singlecellexperiment.io.h5ad module

singlecellexperiment.io.h5ad.read_h5ad(path: str) → SingleCellExperiment

Create a SingleCellExperiment from a H5AD file.

Parameters:

path – Path to a H5AD file.

Returns:

A SingleCellExperiment object.

singlecellexperiment.io.tenx module

singlecellexperiment.io.tenx.read_tenx_h5(path: str, realize_assays: bool = False) → SingleCellExperiment

Read 10X H5 file as SingleCellExperiment.

Note: Currently only supports version 3 of the 10X H5 format.

Parameters:

• path – Path to 10x H5 file.

• realize_assays – Whether to realize assays into memory. Defaults to False.

Returns:

A single-cell experiment object.

singlecellexperiment.io.tenx.read_tenx_mtx(path: str) → SingleCellExperiment

Read 10X Matrix market directory as SingleCellExperiment.

Parameters:

path –

Path to 10X MTX directory.

Directory must contain matrix.mtx, and optionally a genes.tsv to represent featires and barcodes.tsv for cell annotations.

Returns:

A single-cell experiment object.

Module contents