MethScope Data — test fixtures, reproducibility archive

Companion data repo for methscope-cli. This repo carries no models — only small test data. Every model and reference lives on HuggingFace at zhou-lab/methscope, with its description (the HuggingFace model card and the methscope-cli documentation) and its published digest in the YAME registry, so nothing here needs updating when a model does. What stays in git: small test fixtures (test/) used by the examples, and the MRMP-construction reproducibility archive (tag v1).

Test fixtures (test/)

Small query .cg fixtures used by the methscope-cli README/examples: typed cells (human_hg38_celltypes.cg), simulated deconvolution mixtures, an upscale input + truth (human_hg38_test.cg, human_hg38_test.truth.cg), and one small reference so mrmp-build is runnable without the 2.3 GB atlas.

test/human_hg38_immune_mixture.cg — simulated deconvolution mixtures with exact known truths, blended from a deconvolution reference's own class pools. Record names encode composition and sparsity (e.g. mac70_mono30_2pow22 = Macrophage 0.70 / Mono 0.30 at 2^22 binarized CpGs, 1 read each), so each record checks an answer rather than merely producing one. The sparsest rung sits deliberately at the depth where single draws become seed-dependent.

test/human_hg38_40_celltypes_chr20.cg — 40 Loyfer cell types, chr20 only (773,477 CpGs, 40 MB). mrmp-build packs a pattern as a base-3 uint64 and 3^40 < 2^64 < 3^41, so 40 samples is the hard ceiling; chr20 keeps it small enough to ship. The shipped .cg.idx is the sample list; rebuild from the lab store by subsetting those samples from 2023_Loyfer.cg and taking the chr20 row block (recipe in the MethScope lab journal).

test/SHA256SUMS records the digest of every fixture (sha256sum -c SHA256SUMS). It is a convenience for anyone verifying by hand: methscope fetch does not read it, because each digest is compiled into the tool's registry, so a download is checked against something the binary already held rather than against a file served by the same host.

Reproducibility archive (tag v1)

The full MRMP definition sets (*.cm), pattern-definition tables (*_def*), and legacy deconvolution references (*_ref.rds) are archived at tag v1 (git checkout v1). MRMP construction recipes live in the MethScope lab journal (20251216_methscope.org).

License

The data in this repository, at every tag (v1 through v4) and on main, are released under the Creative Commons Attribution 4.0 International license (CC BY 4.0). Files derived from third-party datasets (see Sources) remain subject to the original datasets' terms as well; cite the original studies when you use them. The pretrained models on HuggingFace are under the CHOP academic BSD-2 license (see the model card), and the software under the methscope-cli license.

Sources

The fixtures, the archived MRMP sets and the pretrained models derive from:

• Loyfer et al. 2023, Nature 613:355-364, human cell-type WGBS atlas (GEO GSE186458): human_hg38_celltypes.cg, human_hg38_40_celltypes_chr20.cg, the hg38_Loyfer* and hg38_LoyferPlusZhou sets at v1.
• Liu et al. 2021, Nature 598:120-128, mouse brain single-nucleus methylomes (GEO GSE132489; NeMO): mm10_Liu2021 at v1.
• 1000 Genomes Project: hg38_1KG at v1.
• Zhou et al. 2025, human single-cell methylation atlas: hg38_Zhou2025 and hg38_LoyferPlusZhou at v1, human_hg38_immune_mixture.cg. TODO: publication and accession.
• BLUEPRINT: immune pools in the hg38_33celltypes reference. TODO: confirm the release and its access terms.
• hg38_Sex_20260612 at v1. TODO: record the training data.