Interfacing Seurat with the R tidy universe

Stefano Mangiola, Maria A Doyle, Anthony T Papenfuss, Anthony Mathelier
2021 Bioinformatics  
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 visualisation 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
more » ... ts 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, which allows intuitively interfacing Seurat with dplyr, tidyr, ggplot2 and plotly packages powering efficient data manipulation, integration, and visualisation. Iterative analyses on data subsets are enabled by interfacing with the popular nest-map framework. Availability 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.
doi:10.1093/bioinformatics/btab404 pmid:34028547 fatcat:2clcetyy7reznmwoh62iuyeugu