Interfacing Seurat with the R tidy universe
- Author(s)
- Mangiola, S; Doyle, MA; Papenfuss, AT;
- Details
- Publication Year 2021-05-24,Volume 37,Issue #22,Page 4100-4107
- Journal Title
- Bioinformatics
- 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 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 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.
- Publisher
- Oxford Academic
- Keywords
- *Ecosystem; *Software
- Research Division(s)
- Bioinformatics
- PubMed ID
- 34028547
- Publisher's Version
- https://doi.org/10.1093/bioinformatics/btab404
- Open Access at Publisher's Site
https://doi.org/10.1093/bioinformatics/btab404- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
- Documents
Creation Date: 2021-06-02 01:36:29
Last Modified: 2023-06-14 10:25:54