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 3000 --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 3000 --spot_data False

Run your own data

When using your own data, make sure

• the bulk.csv file must contain one column of gene expression

  	Sample
  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 and Cell_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 three columns of spot name and spatial coordinates. Make sure the column names are correct, i.e., Spot, xcoord and ycoord

  	Spot	xcoord	ycoord
  Cell_1 / Spot_1	Cell_1 / Spot_1	1.2	5.2
  Cell_2 / Spot_2	Cell_1 / Spot_1	5.4	4.3
  ...	...	...	...
  Cell_n / Spot_n	Cell_1 / Spot_1	11.3	6.3

• the sc_data.csv and st_data.csv files are normalized gene expression matrices

Then you will get your results in the output_data folder.

About

Bulk2Space manuscript is unpublished. Should you have any questions, please contact Jie Liao at [email protected], Jingyang Qian at [email protected], or Yin Fang at [email protected]