Bulk2Space

Spatially resolved single-cell deconvolution of bulk transcriptomes using Bulk2Space

python 3.8

Bulk2Space is a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles.

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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 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 two columns of spatial coordinates. Make sure the column names are correct, i.e., xcoord and ycoord

    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 and st_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]

GitHub

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