README.md

SPIDER-paper

Data availability

The user can download the example input from the following link and deposite them in the example_datasets folder.

• Example input data: stored in input_datasets_small.zip.
• Full input data: stored in input_datasets.zip.

Example notebooks

Case 1: Comparison between SPIDER and SpatialDM using the PDAC dataset

Run the notebook PDAD.ipynb with the provided adata from ./example_datasets/PDAC/PDAC_A/. You only need to specify the R_path parameter. The default output folder will be ./results/PDAC/PDAC_A/.

Case 2: Analyses on SPIDER SVIs using the stereo-seq mouse brain dataset

The input adata is stored in the /saw/mouse/ folder in input_datasets_small.zip. Run the notebook SAW.ipynb (need to specify the R_path parameter). The default output folder is ./results/saw/mouse/. To skip the actual running time for this large dataset, the user can also download the output files in saw.zip and put the contents in ./results/saw/mouse/.

Case 3: Analyses on SPIDER SVI patterns using the slide-seq brain dataset

The input adata is stored in the /slide-seq-v2/mousebrain/ folder in input_datasets_small.zip. Run notebooks mouse_brain.ipynb (need to specify the R_path parameter). The default output folder is ./results/slide-seq-v2/mousebrain/. To skip the actual running time for this large dataset, the user can also download the output files in slide-seq-v2.zip and put the contents in ./results/slide-seq-v2/mousebrain/.