univi.datasets.scnmt_gastrulation

univi.datasets.scnmt_gastrulation(**kwargs)

scNMT-seq mouse gastrulation (Argelaguet et al. 2019): RNA, CpG methylation and GpC accessibility (Supplemental Fig. S4).

Published data: https://zenodo.org/records/22885463 (DOI: 10.5281/zenodo.22885463). The three files contain 1,140 paired cells, with 22,084 RNA genes, 18,285 CpG features, and 18,325 GpC features. obs["split"] stores the seed-0 85/5/10 train/validation/test split.

Returns {"rna", "cpg", "gpc"} AnnData objects with RNA counts, CpG/GpC fractions in .X, and success/coverage layers for the beta-binomial likelihoods, as used in the article. Keyword arguments are passed to load(). To parse the original EBI bundle yourself, use load_scnmt_gastrulation_genebody_triplet().