Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.

Autor:	McCarthy DJ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK.; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.; St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia., Campbell KR; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK., Lun AT; CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK., Wills QF; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.; Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2017 Apr 15; Vol. 33 (8), pp. 1179-1186.
DOI:	10.1093/bioinformatics/btw777
Abstrakt:	Motivation: Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization. Results: We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data. The package provides a convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset ready for downstream analysis. scater provides a rich suite of plotting tools for single-cell data and a flexible data structure that is compatible with existing tools and can be used as infrastructure for future software development. Availability and Implementation: The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at http://bioconductor.org/packages/scater . Contact: davis@ebi.ac.uk. Supplementary Information: Supplementary data are available at Bioinformatics online. (© The Author 2017. Published by Oxford University Press.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu