We tested SEDR on DLPFC dataset (12 slices) and compared it with 7 state-of-the art methods:
We highly recommend you to organize the folder as shown below and download the data and scripts into the correct folder.
SEDR_analyses
├── data
│ └── DLPFC
│ └── 151507
│ ├── filtered_feature_bc_matrix.h5
│ ├── metadata.tsv
│ └── spatial
│ ├── scalefactors_json.json
│ ├── tissue_positions_list.csv
│ ├── full_image.tif
│ ├── tissue_hires_image.png
│ └── tissue_lowres_image.png
├── output
│ └── DLPFC
│ └── 151507
├── DLPFC_Seurat.R
└── ...
DLPFC data can be downloaded from SpatialLIBD.
Extract and put data within data/DLPFC folder.
Please notice that the scale_factors_json.json and tissue_positions_list.csv can be found in 10X folder in SpatialLIBD.
Besides, the metadata.tsv we used in SEDR is consistant with BayesSpace.
For convenient, we have put three files within data folder here. You need to move the data folder to where we recommend.
Table of n_clsuters:
Sample_ID | n_clusters |
---|---|
151507 | 7 |
151508 | 7 |
151509 | 7 |
151510 | 7 |
151669 | 5 |
151670 | 5 |
151671 | 5 |
151672 | 5 |
151673 | 7 |
151674 | 7 |
151675 | 7 |
151676 | 7 |
For each sample, run following code
Stero-seq data in SEDR project is included in data folder.