Journal Article

Curated single cell multimodal landmark datasets for R/Bioconductor

Carey, Vincent, Risso, Davide, Righelli, Dario, Waldron, Levi, Eckenrode, Kelly B., Ramos, Marcel, Vanderaa, Christophe, Geistlinger, Ludwig, Culhane, Aedin C., Argelaguet, Ricard, Gatto, Laurent, Morgan, Martin

2023

Overview

The majority of high-throughput single-cell molecular profiling methods quantify RNA expression; however, recent multimodal profiling methods add simultaneous measurement of genomic, proteomic, epigenetic, and/or spatial information on the same cells. The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy availability of landmark datasets using standard data classes. We collected, processed, and packaged publicly available landmark datasets from important single-cell multimodal protocols, including CITE-Seq, ECCITE-Seq, SCoPE2, scNMT, 10X Multiome, seqFISH, and G&T. We integrate data modalities via the MultiAssayExperiment Bioconductor class, document and re-distribute datasets as the SingleCellMultiModal package in Bioconductor's Cloud-based ExperimentHub. The result is single-command actualization of landmark datasets from seven single-cell multimodal data generation technologies, without need for further data processing or wrangling in order to analyze and develop methods within Bioconductor's ecosystem of hundreds of packages for single-cell and multimodal data. We provide two examples of integrative analyses that are greatly simplified by SingleCellMultiModal. The package will facilitate development of bioinformatic and statistical methods in Bioconductor to meet the challenges of integrating molecular layers and analyzing phenotypic outputs including cell differentiation, activity, and disease.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Antibodies / Availability / Biology and life sciences / Cell Differentiation / Cells / Computational Biology / Computer and Information Sciences / CRISPR / Data processing / Datasets / Differentiation (biology) / DNA methylation / Ecosystem / Epigenetics / Epigenomics / Gene expression / Mutation / Phenotype / Physical Sciences / Proteins / Proteomics / Research and analysis methods / RNA / RNA sequencing / Scientific imaging / Software / Spatial data / Standard data / Statistical methods / Statistics