Notebooks ↔ dataset files (Zenodo)
Relative paths below assume the Zenodo bundle is unpacked into
data_external/nguyenlab-il15act-dataset-v1/. Both Zenodo uploads contain the large objects needed to run the pipeline end-to-end: https://zenodo.org/uploads/18838969 and https://zenodo.org/uploads/18842625.
| Notebook | Primary inputs from Zenodo bundle (relative paths) |
|---|---|
nb_01_qc_cell_transcript_filtering.ipynb |
01_processed_anndata/mel_cytokines_andata.h5ad • 00_metadata/ (metadata notes) |
nb_02_compostion_analysis.ipynb |
01_processed_anndata/mel_cytokines_andata.h5ad |
nb_03_tumor_regions_compostion_analysis.ipynb |
02_tables_inputs/sccoda_tumor_regions_input.csv |
nb_04_ligand_receptor_analysis.ipynb |
03_lr_outputs/all_lr_interactions_scores.csv |
nb_05_Collagen_distance_bayes_model.ipynb |
02_tables_inputs/colga_distance_input_table.csv |
nb_06_xenium_codex_alignment.ipynb |
04_codex_slide1/ (Xenium/CODEX exports; TIFF/QPTIFF-derived tables) • 05_spatialdata_zarr/ (raw + corrected .zarr objects) |
nb_07_toxicology_compostion_analysis.ipynb |
01_processed_anndata/tox_cytokines_andata.h5ad |
nb_08_tcell_signature_gene_analysis.ipynb |
02_tables_inputs/skin_tcell_long_counts.csv • 06_models/possion_dge/trace_cd8subsets_day4.pkl |