How to integrate multimodal data is an open problem, especially when aiming to combine data from multiple sources or conditions containing both biological and technical variation. We introduce liam, a flexible model for the simultaneous horizontal and vertical integration of paired single-cell multimodal...
Multimodal single-cell technologies enable the simultaneous collection of diverse data types from individual cells, enhancing our understanding of cellular states. However, the integration of these datatypes and modeling the interrelationships between modalities presents substantial computational and analytical cha...
“Weighted nearest neighbor” analysis integrates multimodal single-cell data • A multimodal reference “atlas” of the circulating human immune system • Identification and validation of novel sources of lymphoid heterogeneity • “Reference-based” mapping of query datasets onto a multimodal atlas...
A growing number of single-cell sequencing platforms enable joint profiling of multiple omics from the same cells. We present Cobolt, a novel method that not only allows for analyzing the data from joint-modality platforms, but provides a coherent framew
Single-cell multimodal datasets have measured various characteristics of individual cells, enabling a deep understanding of cellular and molecular mechanisms. However, multimodal data generation remains costly and challenging, and missing modalities happ
Single-cell multimodal sequencing technologies are developed to simultaneously profile different modalities of data in the same cell. It provides a unique opportunity to jointly analyze multimodal data at the single-cell level for the identification of distinct cell types. A correct clustering result is...
integration of next-generation sequencing with modified patch-clamp techniques is revolutionizing the way to census the primate neocortex, enabling a multimodal neuronal atlas to be established in great detail: (1) single-cell/single-nucleus RNA-seq technology establishes high-throughput transcriptomic ...
Probing histone modifications at a single-cell level in thousands of cells has been enabled by technologies such as single-cell CUT&Tag. Here we describe nano-CUT&Tag (nano-CT), which allows simultaneous mapping of up to three epigenomic modaliti
The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spatial transcriptomics’. Currently however, user-friendly, powerful, and free algorithmic tools for...
32,33,34,35,36,37 Despite remarkable progresses, current strategies still suffer from some limitations: (1) most strategies are limited to dual-specificity with the engagement of a single type of immune cells (e.g., T, natural killer [NK] cell), which is insufficient in confronting the ...