Tutorials¶
The example data¶
The tutorials are based on the example data attached to the CAME package. It is initially saved in compressed form (CAME/came/sample_data.zip), and will be automatically decompressed to the default directory (CAME/came/sample_data/) when necessary, which contains the following files:
gene_matches_1v1_human2mouse.csv (optional)
gene_matches_1v1_mouse2human.csv (optional)
gene_matches_human2mouse.csv
gene_matches_mouse2human.csv
raw-Baron_mouse.h5ad
raw-Baron_human.h5ad
You can access these data by came.load_example_data.
If you tend to apply CAME to analyze your own datasets, you need to prepare at least the last two files for the same species (e.g., cross-dataset integration);
For cross-species analysis, you need to provide another .csv file where the first column contains the genes in the reference species and the second contains the corresponding query homologous genes.
NOTE
The file raw-Baron_human.h5ad is a subsample from the original data for code testing. The resulting annotation accuracy may not be as good as using the full dataset as the reference.