singlecellexperiment.io package¶

Submodules¶

singlecellexperiment.io.h5ad module¶

singlecellexperiment.io.h5ad.read_h5ad(path)[source]¶

Create a SingleCellExperiment from a H5AD file.

Parameters:: path (str) – Path to a H5AD file.
Return type:: SingleCellExperiment
Returns:: A SingleCellExperiment object.

singlecellexperiment.io.tenx module¶

singlecellexperiment.io.tenx.read_tenx_h5(path, realize_assays=False)[source]¶

Read 10X H5 file as SingleCellExperiment.

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

Parameters:

path (str) – Path to 10x H5 file.
realize_assays (bool) – Whether to realize assays into memory. Defaults to False.

Return type:

SingleCellExperiment

Returns:

A single-cell experiment object.

singlecellexperiment.io.tenx.read_tenx_mtx(path)[source]¶

Read 10X Matrix market directory as SingleCellExperiment.

Parameters:

path (str) –

Path to 10X MTX directory.

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

Return type:

SingleCellExperiment

Returns:

A single-cell experiment object.

Module contents¶