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Current best practices in single‐cell RNA‐seq analysis: a tutorial
Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented resolution. The promise of this technology is attracting a growing user base for single‐cell analysis methods. As more analysis tools are becoming available, it is becoming increasingly difficult to navigate this lands...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582955/ https://www.ncbi.nlm.nih.gov/pubmed/31217225 http://dx.doi.org/10.15252/msb.20188746 |
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author | Luecken, Malte D Theis, Fabian J |
author_facet | Luecken, Malte D Theis, Fabian J |
author_sort | Luecken, Malte D |
collection | PubMed |
description | Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented resolution. The promise of this technology is attracting a growing user base for single‐cell analysis methods. As more analysis tools are becoming available, it is becoming increasingly difficult to navigate this landscape and produce an up‐to‐date workflow to analyse one's data. Here, we detail the steps of a typical single‐cell RNA‐seq analysis, including pre‐processing (quality control, normalization, data correction, feature selection, and dimensionality reduction) and cell‐ and gene‐level downstream analysis. We formulate current best‐practice recommendations for these steps based on independent comparison studies. We have integrated these best‐practice recommendations into a workflow, which we apply to a public dataset to further illustrate how these steps work in practice. Our documented case study can be found at https://www.github.com/theislab/single-cell-tutorial. This review will serve as a workflow tutorial for new entrants into the field, and help established users update their analysis pipelines. |
format | Online Article Text |
id | pubmed-6582955 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-65829552019-06-24 Current best practices in single‐cell RNA‐seq analysis: a tutorial Luecken, Malte D Theis, Fabian J Mol Syst Biol Reviews Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented resolution. The promise of this technology is attracting a growing user base for single‐cell analysis methods. As more analysis tools are becoming available, it is becoming increasingly difficult to navigate this landscape and produce an up‐to‐date workflow to analyse one's data. Here, we detail the steps of a typical single‐cell RNA‐seq analysis, including pre‐processing (quality control, normalization, data correction, feature selection, and dimensionality reduction) and cell‐ and gene‐level downstream analysis. We formulate current best‐practice recommendations for these steps based on independent comparison studies. We have integrated these best‐practice recommendations into a workflow, which we apply to a public dataset to further illustrate how these steps work in practice. Our documented case study can be found at https://www.github.com/theislab/single-cell-tutorial. This review will serve as a workflow tutorial for new entrants into the field, and help established users update their analysis pipelines. John Wiley and Sons Inc. 2019-06-19 /pmc/articles/PMC6582955/ /pubmed/31217225 http://dx.doi.org/10.15252/msb.20188746 Text en © 2019 The Authors. Published under the terms of the CC BY 4.0 license This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Reviews Luecken, Malte D Theis, Fabian J Current best practices in single‐cell RNA‐seq analysis: a tutorial |
title | Current best practices in single‐cell RNA‐seq analysis: a tutorial |
title_full | Current best practices in single‐cell RNA‐seq analysis: a tutorial |
title_fullStr | Current best practices in single‐cell RNA‐seq analysis: a tutorial |
title_full_unstemmed | Current best practices in single‐cell RNA‐seq analysis: a tutorial |
title_short | Current best practices in single‐cell RNA‐seq analysis: a tutorial |
title_sort | current best practices in single‐cell rna‐seq analysis: a tutorial |
topic | Reviews |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582955/ https://www.ncbi.nlm.nih.gov/pubmed/31217225 http://dx.doi.org/10.15252/msb.20188746 |
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