mTopic - Figure reproducibility data

This record contains the processed data and intermediate analysis files required to reproduce the figures from the manuscript “Identifying multimodal molecular programs with mTopic”. The deposit includes processed MuData .h5mu objects, RDS objects, CSV summary tables, topic-model outputs, benchmark results, and other intermediate files generated during analysis with mTopic. These files correspond to the P22 mouse brain, human tonsil, and human PBMC datasets analyzed in the manuscript. The P22 mouse brain datasets are derived from Zhang et al. [1], using data from GSE218593 and GSE205055. The human tonsil RNA-protein dataset was obtained from 10x Genomics. The human PBMC ATAC-RNA-protein dataset was obtained from GSE166188 and is associated with Mimitou et al. [2]. This record is intended to support reproducibility of the manuscript figures, including multimodal topic inference, modality-comparison analyses, benchmarking, topic-selection analyses, and figure-generation workflows. Code availability Scripts to reproduce the figures from the manuscript “Identifying multimodal molecular programs with mTopic” are available from the accompanying GitHub repository. References [1] Zhang D, Deng Y, Kukanja P, Agirre E, et al. Spatial epigenome-transcriptome co-profiling of mammalian tissues. Nature. 2023;616(7955):113–122. PMID: 36922587. [2] Mimitou EP, Lareau CA, Chen KY, Zorzetto-Fernandes AL, et al. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nature Biotechnology. 2021;39(10):1246–1258. PMID: 34083792.