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

Ozaki, H.; Hayashi, T.; Mana, U.; Nikaido, I.

doi:10.1101/537936

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bioRxiv · 10.1101/537936

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

Ozaki, H.·Hayashi, T.·Mana, U.·Nikaido, I.

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Abstract

BackgroundRead 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. ResultsHere, 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, including variability of transcribed regions. ConclusionsMillefy 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 a Docker image to help use Millefy on the Jupyter notebook (https://hub.docker.com/r/yuifu/datascience-notebook-millefy).

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Ozaki, H., Hayashi, T., Mana, U., Nikaido, I.. 2019-02-01. Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets. https://doi.org/10.1101/537936

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