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Highly scalable integration and classification of single-cell RNA sequencing data

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Python pacakge: scIntegral

Documentation Status

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.

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