Interfacing Seurat with the R tidy universe

Stefano Mangiola; Maria A Doyle; Anthony T Papenfuss

doi:10.1093/bioinformatics/btab404

Interfacing Seurat with the R tidy universe

Bioinformatics. 2021 Nov 18;37(22):4100-4107. doi: 10.1093/bioinformatics/btab404.

Authors

Stefano Mangiola^{1

2}, Maria A Doyle^{3

4}, Anthony T Papenfuss^{1

2

3

4

5}

Affiliations

¹ Bioinformatics Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia.
² Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia.
³ Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.
⁴ Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia.
⁵ School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010, Australia.

Abstract

Motivation: Seurat is one of the most popular software suites for the analysis of single-cell RNA sequencing data. Considering the popularity of the tidyverse ecosystem, which offers a large set of data display, query, manipulation, integration and visualization utilities, a great opportunity exists to interface the Seurat object with the tidyverse. This interface gives the large data science community of tidyverse users the possibility to operate with familiar grammar.

Results: To provide Seurat with a tidyverse-oriented interface without compromising efficiency, we developed tidyseurat, a lightweight adapter to the tidyverse. Tidyseurat displays cell information as a tibble abstraction, allowing intuitively interfacing Seurat with dplyr, tidyr, ggplot2 and plotly packages powering efficient data manipulation, integration and visualization. Iterative analyses on data subsets are enabled by interfacing with the popular nest-map framework.

Availability and implementation: The software is freely available at cran.r-project.org/web/packages/tidyseurat and github.com/stemangiola/tidyseurat.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Ecosystem*
Software*