laputaliu/cci_evaluation

Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information

cci_evaluation's Issues

Accessing the predicted cell-cell communications for real single-cell RNA seq data in mouse cortex

Hi,

Thanks for making this great benchmarking resource. I see one folder with real example data: example_data/ST_A3_GSM479918.

I am having trouble finding what cell-cell communications were predicted with real single-cell RNA-seq mouse cortex across the different tools?
(https://doi.org/10.1038%2Fnn.4216)

Where in the repo could I find this?

Thanks!

When run Step 1，prepare_ip_dis_sinkhorn2.py reported the error

Hello，The CCI_evaluation is a very good tool for evaluating CCI tools. When I follow the tutorial running "prepare_ip_dis_sinkhorn2.py", the "prepare_ip_dis_sinkhorn2.py" reported the error.
This is the code:
cd ./ST_A3_GSM4797918/data/ip_dis_sinkhorn2 && sudo nohup python /home/njr/CCI-main/scripts/prepare_ip_dis_sinkhorn2.py -c ../processed/st_counts.tsv -p ../processed/st_coord.tsv -o ./ &
the st_counts.tsv and st_coord.tsv is inside CCI_evaluation

the error is：

Please，how to solve this？