Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
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, requir...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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Oxford University Press
2017
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| _version_ | 1797097298398806016 |
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| author | McCarthy, D Campbell, K Lun, A Wills, Q |
| author_facet | McCarthy, D Campbell, K Lun, A Wills, Q |
| author_sort | McCarthy, D |
| collection | OXFORD |
| description | 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.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.The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at http://bioconductor.org/packages/scater .davis@ebi.ac.uk.Supplementary data are available at Bioinformatics online. |
| first_indexed | 2024-03-07T04:53:31Z |
| format | Journal article |
| id | oxford-uuid:d5c7de0c-3a03-4874-81a5-e555d3ef1282 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T04:53:31Z |
| publishDate | 2017 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:d5c7de0c-3a03-4874-81a5-e555d3ef12822022-03-27T08:28:35ZScater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in RJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:d5c7de0c-3a03-4874-81a5-e555d3ef1282EnglishSymplectic Elements at OxfordOxford University Press2017McCarthy, DCampbell, KLun, AWills, QSingle-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.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.The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at http://bioconductor.org/packages/scater .davis@ebi.ac.uk.Supplementary data are available at Bioinformatics online. |
| spellingShingle | McCarthy, D Campbell, K Lun, A Wills, Q Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R |
| title | Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R |
| title_full | Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R |
| title_fullStr | Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R |
| title_full_unstemmed | Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R |
| title_short | Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R |
| title_sort | scater pre processing quality control normalization and visualization of single cell rna seq data in r |
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