| --- |
| license: mit |
| task_categories: |
| - other |
| tags: |
| - biology |
| - gene-regulatory-networks |
| - single-cell |
| - glioblastoma |
| - perturbation |
| - grn-inference |
| size_categories: |
| - 10K<n<100K |
| --- |
| |
| # scRegNet Data & Results |
|
|
| Processed data and results for **scRegNet**: perturbation-calibrated gene representations |
| for context-specific gene regulatory network inference in glioblastoma. |
|
|
| **Code**: [github.com/mmTheBest/scRegNet](https://github.com/mmTheBest/scRegNet) |
|
|
| ## Contents |
|
|
| ### Processed Data (`data/processed/`) |
|
|
| | File | Description | Size | |
| |------|-------------|------| |
| | `gene_universe.json` | G\* gene universe (18,716 genes) | 252 KB | |
| | `hgfb_raw.npz` | H-GFB features (18,716 × 1,152) | 83 MB | |
| | `microglia_labels.npz` | Microglia perturbation labels (38 regulators) | 800 KB | |
| | `k562_labels.npz` | K562 perturbation labels (9,611 regulators) | 19 MB | |
| | `embeddings/*.npz` | 6 embedding sources (18,716 × 256 each) | 116 MB | |
| | `atlas/celltype_means.npz` | Cell-type mean expression (11 types) | 784 KB | |
| | `atlas/neftel_subtypes.npz` | Neftel subtype means (6 subtypes) | 3.2 MB | |
| | `validation/*.json` | ChIP-Atlas, DoRothEA, TRRUST, canonical TFs | 9 MB | |
| | `validation/depmap_ceres.npz` | DepMap CERES scores (50 GBM lines) | — | |
| | `validation/msigdb_genesets.json` | MSigDB gene sets (7,540 sets) | — | |
|
|
| ### Results (`results/`) |
|
|
| | Directory | Description | |
| |-----------|-------------| |
| | `stage_b/` | Stage B model outputs (6 embeddings + 3 controls) | |
| | `stage_c/` | Stage C GRN predictions (6 sources × 17 contexts, parquet) | |
| | `competing/` | 8 competing method outputs | |
| | `experiments/exp_1-9/` | All 9 experiment results (JSON) | |
| | `figures/` | 7 main + 6 extended figures (PDF + PNG) | |
|
|
| ### Not Included (Regeneratable) |
|
|
| - Raw count matrices (`data/processed/stage_c/`, 4.3 GB) — regenerate from GEO GSE274546 |
| - Per-cell expression matrices (`data/processed/atlas/celltype_expr/`, 1.8 GB) — regenerate via `05a_prepare_atlas.py` |
|
|
| ## Usage |
|
|
| ```python |
| from huggingface_hub import snapshot_download |
| |
| # Download everything |
| snapshot_download("mm1109/scRegNet", repo_type="dataset", local_dir="./scRegNet-data") |
| |
| # Load embeddings |
| import numpy as np |
| data = np.load("scRegNet-data/data/processed/embeddings/geneformer.npz") |
| embeddings = data["embeddings"] # (18716, 256) |
| genes = data["genes"] # (18716,) |
| |
| # Load GRN predictions |
| import pandas as pd |
| grn = pd.read_parquet("scRegNet-data/results/stage_c/geneformer.parquet") |
| ``` |
|
|
| ## License |
|
|
| MIT |
|
|
