Processing single-cell RNA-seq datasets using SingCellaR

Guanlin Wang; Wei Xiong Wen; Adam J. Mead; Anindita Roy; Bethan Psaila; Supat Thongjuea

STAR Protocols (Jun 2022)

Processing single-cell RNA-seq datasets using SingCellaR

Guanlin Wang,
Wei Xiong Wen,
Adam J. Mead,
Anindita Roy,
Bethan Psaila,
Supat Thongjuea

Affiliations

Guanlin Wang: MRC Molecular Haematology Unit, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; Centre for Computational Biology, Medical Research Council Weatherall Institute of Molecular Medicine (MRC WIMM), University of Oxford, Oxford OX3 9DS, UK
Wei Xiong Wen: MRC Molecular Haematology Unit, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; Centre for Computational Biology, Medical Research Council Weatherall Institute of Molecular Medicine (MRC WIMM), University of Oxford, Oxford OX3 9DS, UK
Adam J. Mead: MRC Molecular Haematology Unit, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
Anindita Roy: MRC Molecular Haematology Unit, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; Department of Paediatrics, Children’s Hospital, John Radcliffe Hospital, and MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
Bethan Psaila: MRC Molecular Haematology Unit, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
Supat Thongjuea: MRC Molecular Haematology Unit, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; Centre for Computational Biology, Medical Research Council Weatherall Institute of Molecular Medicine (MRC WIMM), University of Oxford, Oxford OX3 9DS, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK; Corresponding author

Journal volume & issue: Vol. 3, no. 2
p. 101266

Abstract

Read online

Summary: Single-cell RNA sequencing has led to unprecedented levels of data complexity. Although several computational platforms are available, performing data analyses for multiple datasets remains a significant challenge. Here, we provide a comprehensive analytical protocol to interrogate multiple datasets on SingCellaR, an analysis package in R. This tool can be applied to general single-cell transcriptome analyses. We demonstrate steps for data analyses and visualization using bespoke pipelines, in conjunction with existing analysis tools to study human hematopoietic stem and progenitor cells.For complete details on the use and execution of this protocol, please refer to Roy et al. (2021).

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

About the journal

Abstract

Keywords