example.sh

#!/usr/bin/bash

## download example data from https://noble.gs.washington.edu/~ranz0/Sunbear/data/ to Sunbear/data/ directory
cd Sunbear
mkdir data/
cd data
wget https://noble.gs.washington.edu/~ranz0/Sunbear/data/example_single_rna.h5ad
wget https://noble.gs.washington.edu/~ranz0/Sunbear/data/example_multi_rna.h5ad
wget https://noble.gs.washington.edu/~ranz0/Sunbear/data/example_multi_atac.h5ad

## train model
cd ..
## example 1: temporal infernece and then predict temporal changes of cells in Muscles around E16
rna_h5ad=data/example_single_rna.h5ad
python bin/sunbear.py --domain rna --rna_h5ad $rna_h5ad --batch batch --condition sex --predict temporal --ct_query Muscle_cells --targettime 16

## example 2: compare expression difference between conditions (i.e., sexes) and return sex-difference prediction for each cell type at E16
rna_h5ad=data/example_single_rna.h5ad
python bin/sunbear.py --domain rna --rna_h5ad $rna_h5ad --batch batch --condition sex --targettime 16 --predict diffexp_condition --sourcecondition M --targetcondition F 

## example 3: cross-modality temporal inference and return temporal profile changes for cells in Hindbrain trajectory around E8.25
rna_h5ad=data/example_multi_rna.h5ad
atac_h5ad=data/example_multi_rna.h5ad
python bin/sunbear.py --domain multi --rna_h5ad $rna_h5ad --atac_h5ad $atac_h5ad --batch batch --predict temporal --time_range 0.1 --targettime 8.25 --ct_query Hindbrain