| --- |
| license: mit |
| tags: |
| - spatial-transcriptomics |
| - gene-regulatory-network |
| - xenium |
| - spacetravlr |
| - mouse |
| - skin |
| pretty_name: SpaceTravLR outputs |
| size_categories: |
| - 100B<n<1T |
| --- |
| |
| # SpaceTravLR dataset hub |
|
|
| Precomputed [SpaceTravLR](https://github.com/Koushul/SpaceTravLR_rust) outputs: per-gene beta matrices (`*_betadata.feather`), run metadata, and optional per-sample `.h5ad` exports. |
|
|
| ## Layout |
|
|
| ``` |
| spacetravlr/ |
| ├── tonsil/ # placeholder / demo gene outputs |
| └── xenium_skin_mixed/ |
| ├── run.toml # shared training config for this cohort |
| ├── manifest.json # sample index and upload metadata |
| ├── sample12/ |
| ├── sample13/ |
| ├── sample14/ |
| ├── sample15/ |
| └── sample16/ |
| ``` |
|
|
| Each `xenium_skin_mixed/sample*/` directory contains: |
|
|
| | File / folder | Description | |
| |---|---| |
| | `*_betadata.feather` | Per-modulator beta matrices from SpaceTravLR training | |
| | `sample*.h5ad` | Condition-filtered AnnData export for the sample | |
| | `sample*.csv` | Summary table for the run | |
| | `condition_label.txt` | Condition identifier | |
| | `spacetravlr_run_repro.toml` | Reproducibility config (paths rewritten on download) | |
| | `spacetravlr_run_summary.html` | HTML training summary | |
| | `log/` | Training logs | |
|
|
| **Not uploaded:** `perturbations/` folders (in-silico perturbation grids). |
|
|
| ## Cohort: `xenium_skin_mixed` |
|
|
| Mouse skin Xenium data with mixed samples. Training used `xenium_skin_mixed.h5ad` with `sample_id` as the condition column and `cell_type_int` as the cluster annotation. |
|
|
| | Sample | Approx. size | Beta files | |
| |--------|-------------:|-----------:| |
| | sample12 | 59 GB | 2,809 | |
| | sample13 | 103 GB | 2,807 | |
| | sample14 | 66 GB | 2,810 | |
| | sample15 | 100 GB | 2,801 | |
| | sample16 | 89 GB | 2,801 | |
|
|
| ## Download |
|
|
| ```bash |
| # Entire xenium_skin_mixed cohort |
| hf download Koushul/spacetravlr xenium_skin_mixed --repo-type dataset --local-dir ./spacetravlr |
| |
| # Single sample |
| hf download Koushul/spacetravlr xenium_skin_mixed/sample12 --repo-type dataset --local-dir ./sample12 |
| ``` |
|
|
| ## Usage with SpaceTravLR |
|
|
| Point `spatial_viewer` or `spacetravlr-perturb` at a downloaded sample directory containing `*_betadata.feather` and the matching `spacetravlr_run_repro.toml`. |
|
|
| ## Citation |
|
|
| If you use these outputs, please cite SpaceTravLR and the underlying Xenium skin dataset. |
|
|
