Bulk2Space
Spatially resolved single-cell deconvolution of bulk transcriptomes using Bulk2Space
Bulk2Space is a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles.
Installation
For bulk2space, the python version need is over 3.8. If you have installed Python3.6 or Python3.7, consider installing Anaconda, and then you can create a new environment.
conda create -n bulk2space python=3.8.5
conda activate bulk2space
cd bulk2space
pip install -r requirements.txt
Usage
Run the demo data
If you choose the spatial barcoding-based data(like 10x Genomics or ST) as spatial reference, run the following command:
python bulk2space.py --project_name test1 --data_path example_data/demo1 --input_sc_meta_path demo1_sc_meta.csv --input_sc_data_path demo1_sc_data.csv --input_bulk_path demo1_bulk.csv --input_st_data_path demo1_st_data.csv --input_st_meta_path demo1_st_meta.csv --BetaVAE_H --epoch 10 --spot_data True
else, if you choose the image-based in situ hybridization data(like MERFISH, SeqFISH, and STARmap) as spatial reference, run the following command:
python bulk2space.py --project_name test2 --data_path example_data/demo2 --input_sc_meta_path demo2_sc_meta.csv --input_sc_data_path demo2_sc_data.csv --input_bulk_path demo2_bulk.csv --input_st_data_path demo2_st_data.csv --input_st_meta_path demo2_st_meta.csv --BetaVAE_H --epoch 10 --spot_data False
Run your own data
When using your own data, make sure
-
the
bulk.csv
file must contain one column of gene expressionSample Gene1 5.22 Gene2 3.67 ... ... GeneN 15.76 -
the
sc_meta.csv
file must contain two columns of cell name and cell type. Make sure the column names are correct, i.e.,Cell
andCell_type
Cell Cell_type Cell_1 Cell_1 T cell Cell_2 Cell_2 B cell ... ... ... Cell_n Cell_n Monocyte -
the
st_meta.csv
file must contain at least two columns of spatial coordinates. Make sure the column names are correct, i.e.,xcoord
andycoord
xcoord ycoord Cell_1 / Spot_1 1.2 5.2 Cell_2 / Spot_2 5.4 4.3 ... ... ... Cell_n / Spot_n 11.3 6.3 -
the
sc_data.csv
andst_data.csv
files are gene expression matrices
Then you will get your results in the output_data
folder.
For more details, see user guide in the document.
About
Bulk2Space manuscript is under major revision. Should you have any questions, please contact Jie Liao at [email protected], Jingyang Qian at [email protected], or Yin Fang at [email protected]