MethScope — pretrained models
Pretrained models for methscope-cli:
ultra-fast analysis of sparse DNA methylomes via MRMP (Most Recurrent Methylation
Pattern) encoding. Each model is a single self-contained bundle that already
carries its MRMP feature definition (and labels / signature), so a query .cg
runs directly — no separate annotation files.
Fetch & run
# fetch one model (or --local-dir models to grab all)
hf download zhou-lab/methscope hg38_celltype.ubjx --local-dir .
methscope predict query.cg hg38_celltype.ubjx # cell type / label
methscope deconv mixture.cg hg38_65celltypes.refx # cell-type proportions (NNLS)
methscope upscale -o out.cg hg38_wg.updecx query.cg # genome-wide CpG upscaling
methscope inspect hg38_sex.ubjx # framework, labels, features
Small query .cg test fixtures (typed cells, a deconvolution mixture, an
upscale input + truth) live in the GitHub repo
zhou-lab/methscope_data under
test/, alongside this catalog and the MRMP-construction reproducibility archive.
Models
| file | task | framework | labels / notes |
|---|---|---|---|
hg38_wg.updecx |
whole-genome CpG upscaling | UPDEC2 |
all 29,401,795 hg38 CpGs; the primary upscaler (2.8 GB) |
hg38_10k1.updecx |
CpG upscaling (single block) | MLP decoder | block 10k1 (10,000 CpGs); small demo model |
hg38_celltype.ubjx |
cell-type annotation | xgboost | 62 human cell types |
mm10_celltype.ubjx |
cell-type annotation | xgboost | 41 mouse-brain cell types |
hg38_sex.ubjx |
sex prediction | logistic | Female, Male (XCI Xa_hi/Xa_lo markers) |
hg38_65celltypes.refx |
cell-type deconvolution (NNLS) | refx | 65 types = 58 Zhou + 7 Loyfer organ/blood; split MRMP, 15,300 patterns |
methscope inspect <model> prints the exact framework, full label list, and (for
linear models) per-feature weights. Classifiers carry a required framework kind
mark (xgboost / threshold / logistic); predict rejects an unmarked
bundle. Upscale decoders (.updecx) run via upscale, deconvolution references
(.refx, kind=refx) via deconv.
See the methscope-cli documentation for the full command reference and runnable examples.