Interfacing Seurat with the R tidy universe

Abstract

AbstractMotivationSeurat 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 visualisation utilities, a great opportunity exists to interface the Seurat object with the tidyverse. This gives the large data science community of tidyverse users the possibility to operate with a familiar grammar.ResultsIn order to provide Seurat with a tidyverse-oriented interface without compromising on efficiency, we developed tidyseurat, a light-weight adapter to the tidyverse. Cell information is automatically displayed as a tibble abstraction, which interfaces Seurat with dplyr, tidyr, ggplot2 and plotly packages powering efficient data manipulation, integration and visualisation. Iterative analyses on data subsets is enabled by interfacing with the popular nest-map framework.Availability and implementationThe software is freely available at cran.r-project.org/web/packages/tidyseurat/ and github.com/stemangiola/tidyseuratContactStefano Mangiola (mangiola.s@wehi.edu.au) and Anthony T Papenfuss (papenfuss@wehi.edu.au).