Python pacakge: scIntegral

Installation

scintegral can be installed using pip

pip install scintegral

Basic Usage

scIntegral's cell classifier can be loaded through

import scintegral.classifer as scint_classifier
import scintegral.utils as scint_utils

scIntegral requires a marker information for each cell-type. Given a python dictionary of the following format,

marker_dict = {
    ...
    'Fibroblasts':['Col3a1', 'Col8a1']
    ...
}

run

scint_utils.marker_input_creator(marker_dict)

which returns a onehot pandas dataframe in which scIntegral takes as an input.

Finally, to run scIntegral's cell classifier,

scint_classifier.classify_cells(...)

The arguments can be found at the documentation page.