scSemiProfiler_dev.initial_setup.initsetup

scSemiProfiler_dev.initial_setup.initsetup(name, bulk, normed, geneselection, batch)

Initial setup of the semi-profiling pipeline, including processing the bulk data, clustering for finding the initial representatives.

Parameters

• name (str) – Project name.

• bulk (str) – Path to bulk data.

• normed (str) – Whether the data has been library size normed or not.

• geneselection (str) – Whether to perform gene selection.

• batch (int) – Representative selection batch size.

Example

>>> import scSemiProfiler
>>> name = 'runexample'
>>> bulk = 'example_data/bulkdata.h5ad'
>>> normed = 'yes'
>>> geneselection = 'no'
>>> batch = 2
>>> scSemiProfiler.initsetup(name, bulk,normed,geneselection,batch)

Return type

None