TY - JOUR
T1 - Interfacing Seurat with the R tidy universe
AU - Mangiola, Stefano
AU - Doyle, Maria A.
AU - Papenfuss, Anthony T.
N1 - Publisher Copyright:
© 2021 The Author(s). Published by Oxford University Press.
PY - 2021/11/15
Y1 - 2021/11/15
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85151238486&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btab404
DO - 10.1093/bioinformatics/btab404
M3 - Article
C2 - 34028547
AN - SCOPUS:85151238486
SN - 1367-4803
VL - 37
SP - 4100
EP - 4107
JO - Bioinformatics
JF - Bioinformatics
IS - 22
ER -