README.md

metadata

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 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

# 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.