Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
Center for Artificial Intelligence Research, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
BMC Genomics. 2020 Mar 3;21(1):177. doi: 10.1186/s12864-020-6542-z.
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.
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.
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).
RNA 测序数据的读覆盖反映了基因表达和 RNA 处理事件。单细胞 RNA 测序（scRNA-seq）方法，特别是“全长”方法，提供了许多单个细胞的读覆盖，并有可能揭示 RNA 转录和处理中的细胞异质性。然而，适合突出读覆盖细胞间异质性的可视化工具仍然缺乏。
在这里，我们开发了 Millefy，这是一种用于可视化 scRNA-seq 数据在基因组背景下读覆盖的工具。Millefy 旨在一次在基因组背景下显示所有单个细胞的读覆盖，并突出读覆盖的细胞间异质性。通过将所有细胞的读覆盖可视化作为热图，并根据扩散图动态重新排列细胞，Millefy 有助于发现读覆盖的“局部”区域特异性、细胞间异质性。我们将 Millefy 应用于小鼠胚胎干细胞和三阴性乳腺癌的 scRNA-seq 数据集，并显示了转录区域的可变性，包括反义 RNA、3'UTR 长度和增强子 RNA 转录。
Millefy 简化了使用 scRNA-seq 数据检查 RNA 转录和处理事件中的细胞异质性。Millefy 作为一个 R 包（https://github.com/yuifu/millefy）和一个用于 Jupyter Notebook 的 Docker 映像提供（https://hub.docker.com/r/yuifu/datascience-notebook-millefy）。
