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license: agpl-3.0
library_name: methscope
tags:
  - dna-methylation
  - methylation
  - wgbs
  - single-cell
  - imputation
  - deconvolution
  - cell-type-annotation

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.