2022
DOI: 10.1093/bioinformatics/btac220
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MOJITOO: a fast and universal method for integration of multimodal single-cell data

Abstract: Motivation The advent of multi-modal single-cell sequencing techniques have shed new light on molecular mechanisms by simultaneously inspecting transcriptomes, epigenomes and proteomes of the same cell. However, to date, the existing computational approaches for integration of multimodal single-cell data are either computationally expensive, require the delineation of parameters or can only be applied to particular modalities. Results … Show more

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Cited by 14 publications
(11 citation statements)
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“…2). While some benchmarking strategies have been developed for assessing analysis and visualization of well-clustered data, such as silhouette score or adjusted Rand index score [48], we designed new benchmarks related to the visualization of developmental multimodal data and transitions between cells (Fig. 3, Supplementary Fig.…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…2). While some benchmarking strategies have been developed for assessing analysis and visualization of well-clustered data, such as silhouette score or adjusted Rand index score [48], we designed new benchmarks related to the visualization of developmental multimodal data and transitions between cells (Fig. 3, Supplementary Fig.…”
Section: Resultsmentioning
confidence: 99%
“…It uses stochastic variational inference [46, 47] for scalability of the parameter inference. Other approaches based on integrative methods exist, such as MOJITOO [48] that uses canonical correlation analysis to find low-dimensional multimodal data representation.…”
Section: Introductionmentioning
confidence: 99%
“…SHARE-seq ( Ma et al , 2020 ) and 10× Multiome], this integration step can be skipped. Here, users only need to create a joint embedding of cells by using for example the CCA integration from MOJITOO ( Cheng et al , 2022 ).…”
Section: Methodsmentioning
confidence: 99%
“…Finally, scMEGA merges the data for each of the pairs by extracting gene expression from scRNAseq and chromatin accessibility from scATAC-seq. Of note, this step can be skipped in case single-cell multimodal protocols (e.g., SHARE-seq [16] and 10X Multiome) were employed and a joint embedding of the modalities is available, such as provided by MOJI-TOO [17].…”
Section: Data Integrationmentioning
confidence: 99%