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README.md

@@ -1,73 +1,57 @@
 ---
-license: mit
-library_name: enhancer-designer
+library_name: regrex
+license: other
+license_name: allen-institute-software-license
+license_link: LICENSE
 tags:
-  - pytorch
-  - lightning
-  - genomics
-  - neuroscience
-  - regulatory-genomics
-  - sequence-modeling
-  - enhancer-design
-  - sequence-to-function
-  - basal-ganglia
-  - macaque
-  - dilated-cnn
-pretty_name: Dilated CNN Macaque Basal Ganglia model
+- pytorch
+- lightning
+- genomics
+- regrex
+- neuroscience
+- regulatory-genomics
+- sequence-to-function
+- basal-ganglia
+- macaque
+- dilated_cnn
 ---
 
 # AllenInstitute/BG-macaque-dilatedCNN
 
-Dilated CNN trained on macaque (*Macaca mulatta*) basal ganglia chromatin accessibility data across 58 cell type tracks. Part of the DNA sequence modeling resources associated with the basal ganglia cell atlas package. Published in [Johansen, Fu et al., 2025](https://doi.org/10.64898/2025.12.15.694496).
+Dilated CNN trained on macaque (*Macaca mulatta*) basal ganglia chromatin accessibility across 58 cell-type tracks. Part of the DNA sequence-modeling resources for the basal ganglia cell atlas. Published in [Johansen, Fu et al., 2025](https://doi.org/10.64898/2025.12.15.694496).
 
-## Model Details
-
-| Field | Value |
-|---|---|
-| Architecture | Dilated CNN |
-| Species | *Macaca mulatta* (macaque) |
-| Brain region | Basal ganglia |
-| Number of tracks | 58 |
-| Framework | PyTorch Lightning |
-| Checkpoint format | `.ckpt` |
+### Background
+Learns cis-regulatory sequence logic underlying basal ganglia cell-type specialization from snATAC-seq accessibility profiles. Use it to score candidate enhancers, run in silico mutagenesis, or guide cell-type-specific sequence design.
 
-## Background
+### Availability
+Currently private. RegRex (formerly `enhancer-designer`) is an internal Allen Institute tool with a public release planned. For early access contact Kasia Kedzierska (kasia.kedzierska@alleninstitute.org).
 
-This model learns cis-regulatory sequence logic underlying basal ganglia cell type specialization from snATAC-seq-derived accessibility profiles. It can be used to score candidate enhancer sequences, run in silico mutagenesis, or guide sequence design for specific cell types.
-
-For broader context on the associated multiomic studies and the consensus cell type taxonomy used to define tracks, see the [BG Cell Atlas sequence modeling repository](https://huggingface.co/AllenInstitute/BG-cell-atlas-sequence-modeling).
+## Model Details
 
-## Availability
+- **Architecture:** dilated_cnn
+- **Species:** macaque
+- **Number of tracks:** 58
+- **Framework:** PyTorch Lightning
+- **Checkpoint format:** Lightning .ckpt
 
-This repository is currently private. The `enhancer-designer` codebase is an internal Allen Institute tool with a public release planned in the near future.
+## Target Tracks
 
-To request early access, please contact **Kasia Kedzierska** at kasia.kedzierska@alleninstitute.org.
+- AMY-SLEA-BNST_D1_GABA
+- AMY-SLEA-BNST_GABA
+- Astrocyte
+- BAM
+- BF_SKOR1_Glut
+- COP
+- Endo
+- Ependymal
+- GPe-NDB-SI_LHX6-LHX8-GBX1_GABA
+- GPe_MEIS2-SOX6_GABA
+- ... (48 more)
 
 ## Usage
 
 ```python
-from enhancerdesigner.models import load_model
-
-model = load_model("AllenInstitute/BG-macaque-dilatedCNN")
-```
-
-## Target Tracks
-
-The full list of 58 tracks is accessible programmatically after loading:
+from regrex.models import load_model
 
-```python
 model = load_model("AllenInstitute/BG-macaque-dilatedCNN")
-print(model.target_names)
 ```
-
-## Citation
-
-```bibtex
-@article{Johansen2025,
-  title   = {Cross-species consensus atlas of the primate basal ganglia},
-  author  = {Johansen, Nelson and Fu, Yuanyuan and others},
-  journal = {bioRxiv},
-  year    = {2025},
-  doi     = {10.64898/2025.12.15.694496}
-}
-```