Linking Genetic Risk to Disease-Relevant Cellular States via Metacell-Informed Modeling with ICePop

This dataset contains the processed data used in the analyses of the paper: “Linking Genetic Risk to Disease-Relevant Cellular States via Metacell-Informed Modeling with ICePop” (https://doi.org/10.64898/2026.04.01.715877). Code and notebooks to reproduce the analyses are available at: https://github.com/krishnanlab/icepop_analysis The ICePop Python package is available at: https://github.com/krishnanlab/icepop This dataset includes the following components: simulation.tar.gz: TM_subset_cnt.h5ad: subsampled single cell data from Tabula Muris FACS. causal_simulation/: simulated disease signal with varying the fraction of causal genes varying the noise variance varying the signal scaling factors causal_simulation_synthetic/: simulated disease signal with varying disease signal heterogeneity within synthetic cell types null_simulation/: simulated null signal by permuting MAGMA gene-level z-scores magma.tar.gz: magmaz/: MAGMA-derived z-scores for all diseases/traits analyzed in this study. Corresponding disease/trait metadata are provided in Supplementary Data 1 TM_FACS.tar.gz: TM_FACS_cnt.h5ad Processed single-cell RNA-seq data count from Tabula Muris FACS. Raw data were obtained from: https://doi.org/10.6084/m9.figshare.5829687.v7 Renamed cell types and general tissue/system categories are provided in Supplementary Data 1 mouse_colon.tar.gz: mouse_colon_cnt.h5ad: Single-cell RNA-seq data of mouse colon enteric cells from Drokhlyansky et al. Cell 2020. Raw data were obtained from the Single Cell Portal (SCP1038) SFARI-Gene_genes_01-13-2025release_03-27-2025export.csv: SFARI gene scores Scores were downloaded from https://gene.sfari.org/database/human-gene/ Supp_data.tar.gz: Supplementary_data1.xlsx: 81 disease/trait metadata used in this study 120 cell types and general tissue/system categories for TM FACS dataset Supplementary_data2.xlsx: Disease–cell type association results from the TM FACS scan across 81 diseases/traits, generated using ICePop, seismic, and scDRS. Supplementary_data3.xlsx: ASD associated celltype results generated using ICePop, seismic and scDRS