Dataset Information

Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets.

ABSTRACT: BACKGROUND:Read coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly "full-length" ones, provide read coverage of many individual cells and have the potential to reveal cellular heterogeneity in RNA transcription and processing. However, visualization tools suited to highlighting cell-to-cell heterogeneity in read coverage are still lacking. RESULTS:Here, we have developed Millefy, a tool for visualizing read coverage of scRNA-seq data in genomic contexts. Millefy is designed to show read coverage of all individual cells at once in genomic contexts and to highlight cell-to-cell heterogeneity in read coverage. By visualizing read coverage of all cells as a heat map and dynamically reordering cells based on diffusion maps, Millefy facilitates discovery of "local" region-specific, cell-to-cell heterogeneity in read coverage. We applied Millefy to scRNA-seq data sets of mouse embryonic stem cells and triple-negative breast cancers and showed variability of transcribed regions including antisense RNAs, 3 ' UTR lengths, and enhancer RNA transcription. CONCLUSIONS:Millefy simplifies the examination of cellular heterogeneity in RNA transcription and processing events using scRNA-seq data. Millefy is available as an R package (https://github.com/yuifu/millefy) and as a Docker image for use with Jupyter Notebook (https://hub.docker.com/r/yuifu/datascience-notebook-millefy).

SUBMITTER: Ozaki H

PROVIDER: S-EPMC7053140 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets.

Ozaki Haruka H Hayashi Tetsutaro T Umeda Mana M Nikaido Itoshi I

BMC genomics 20200303 1

<h4>Background</h4>Read coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly "full-length" ones, provide read coverage of many individual cells and have the potential to reveal cellular heterogeneity in RNA transcription and processing. However, visualization tools suited to highlighting cell-to-cell heterogeneity in read coverage are still lacking.<h4>Results</h4>Here, we have developed Millefy, a tool f ...[more]

PMID: 32122302

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Dataset Information

Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets.

Publications

Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets.

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