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

Stefano Mangiola
, Maria A. Doyle
, Anthony T. Papenfuss

Walter and Eliza Hall Institute of Medical Research
University of Melbourne
Peter Maccallum Cancer Centre

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	4100-4107
Number of pages	8
Journal	Bioinformatics
Volume	37
Issue number	22
DOIs	https://doi.org/10.1093/bioinformatics/btab404
Publication status	Published - 15 Nov 2021
Externally published	Yes

Access to Document

10.1093/bioinformatics/btab404

Cite this

@article{4cd62a4983fb4066af058a762d0738f8,

title = "Interfacing Seurat with the R tidy universe",

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.",

author = "Stefano Mangiola and Doyle, \{Maria A.\} and Papenfuss, \{Anthony T.\}",

note = "Publisher Copyright: {\textcopyright} 2021 The Author(s). Published by Oxford University Press.",

year = "2021",

month = nov,

day = "15",

doi = "10.1093/bioinformatics/btab404",

language = "English",

volume = "37",

pages = "4100--4107",

journal = "Bioinformatics",

issn = "1367-4803",

number = "22",

}

TY - JOUR

T1 - Interfacing Seurat with the R tidy universe

AU - Mangiola, Stefano

AU - Doyle, Maria A.

AU - Papenfuss, Anthony T.

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 - https://www.scopus.com/pages/publications/85151238486

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 -

Interfacing Seurat with the R tidy universe

Abstract

Access to Document

Other files and links

Fingerprint

Cite this