metadata
library_name: regrex
license: other
license_name: allen-institute-software-license
license_link: LICENSE
tags:
- 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 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.
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.
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).
Model Details
- Architecture: dilated_cnn
- Species: macaque
- Number of tracks: 58
- Framework: PyTorch Lightning
- Checkpoint format: Lightning .ckpt
Target Tracks
- 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
from regrex.models import load_model
model = load_model("AllenInstitute/BG-macaque-dilatedCNN")