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Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for researchers. In order to better facilitate selection o...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6034903/ https://www.ncbi.nlm.nih.gov/pubmed/29939984 http://dx.doi.org/10.1371/journal.pcbi.1006245 |
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author | Zappia, Luke Phipson, Belinda Oshlack, Alicia |
author_facet | Zappia, Luke Phipson, Belinda Oshlack, Alicia |
author_sort | Zappia, Luke |
collection | PubMed |
description | As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for researchers. In order to better facilitate selection of appropriate analysis tools we have created the scRNA-tools database (www.scRNA-tools.org) to catalogue and curate analysis tools as they become available. Our database collects a range of information on each scRNA-seq analysis tool and categorises them according to the analysis tasks they perform. Exploration of this database gives insights into the areas of rapid development of analysis methods for scRNA-seq data. We see that many tools perform tasks specific to scRNA-seq analysis, particularly clustering and ordering of cells. We also find that the scRNA-seq community embraces an open-source and open-science approach, with most tools available under open-source licenses and preprints being extensively used as a means to describe methods. The scRNA-tools database provides a valuable resource for researchers embarking on scRNA-seq analysis and records the growth of the field over time. |
format | Online Article Text |
id | pubmed-6034903 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-60349032018-07-19 Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database Zappia, Luke Phipson, Belinda Oshlack, Alicia PLoS Comput Biol Research Article As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for researchers. In order to better facilitate selection of appropriate analysis tools we have created the scRNA-tools database (www.scRNA-tools.org) to catalogue and curate analysis tools as they become available. Our database collects a range of information on each scRNA-seq analysis tool and categorises them according to the analysis tasks they perform. Exploration of this database gives insights into the areas of rapid development of analysis methods for scRNA-seq data. We see that many tools perform tasks specific to scRNA-seq analysis, particularly clustering and ordering of cells. We also find that the scRNA-seq community embraces an open-source and open-science approach, with most tools available under open-source licenses and preprints being extensively used as a means to describe methods. The scRNA-tools database provides a valuable resource for researchers embarking on scRNA-seq analysis and records the growth of the field over time. Public Library of Science 2018-06-25 /pmc/articles/PMC6034903/ /pubmed/29939984 http://dx.doi.org/10.1371/journal.pcbi.1006245 Text en © 2018 Zappia et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Zappia, Luke Phipson, Belinda Oshlack, Alicia Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database |
title | Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database |
title_full | Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database |
title_fullStr | Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database |
title_full_unstemmed | Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database |
title_short | Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database |
title_sort | exploring the single-cell rna-seq analysis landscape with the scrna-tools database |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6034903/ https://www.ncbi.nlm.nih.gov/pubmed/29939984 http://dx.doi.org/10.1371/journal.pcbi.1006245 |
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