cytocraft 0.0.2

The Cytocraft package provides prediction of chromosome conformation based on spatial transcriptomic.

Cytocraft

The Cytocraft package provides prediction of chromosome conformation based on spatial transcriptomic.

Quick Start

Run Cytocraft

This example shows the usage of Cytocraft.

python craft.py ./data/SS200000108BR_A3A4_scgem.Spinal_cord_neuron.csv ./results/ Mouse

Usage

craft.py [-h] [-p PERCENT] [-c CELLTYPE] [--ctkey CTKEY] [--cikey CIKEY] [--seed SEED] gem_path out_path {Human,Mouse,Axolotls,Monkey}

positional arguments:

gem_path Path to gem file

out_path Output path to save results

{Human,Mouse,Axolotls,Monkey} Species of the input data

optional arguments:

-h, --help show this help message and exit

-p, --percent percent of gene for rotation derivation, default: 0.001

-t, --threshold The maximum proportion of np.nans allowed in a column(gene) in W, default: 0.90

-c, --celltype Path of file containing cell types

--ctkey Key of celltype column in the cell type file

--cikey Key of cell id column in the cell type file

--seed Random seed