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Stemformatics: visualize and download curated stem cell data
Stemformatics is an established gene expression data portal containing over 420 public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Developed for the stem cell community, it has a major focus on pluripotency, tissue stem cells, and staged d...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323943/ https://www.ncbi.nlm.nih.gov/pubmed/30407577 http://dx.doi.org/10.1093/nar/gky1064 |
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author | Choi, Jarny Pacheco, Chris M Mosbergen, Rowland Korn, Othmar Chen, Tyrone Nagpal, Isha Englart, Steve Angel, Paul W Wells, Christine A |
author_facet | Choi, Jarny Pacheco, Chris M Mosbergen, Rowland Korn, Othmar Chen, Tyrone Nagpal, Isha Englart, Steve Angel, Paul W Wells, Christine A |
author_sort | Choi, Jarny |
collection | PubMed |
description | Stemformatics is an established gene expression data portal containing over 420 public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Developed for the stem cell community, it has a major focus on pluripotency, tissue stem cells, and staged differentiation. Stemformatics includes curated ‘collections’ of data relevant to cell reprogramming, as well as hematopoiesis and leukaemia. Rather than simply rehosting datasets as they appear in public repositories, Stemformatics uses a stringent set of quality control metrics and its own pipelines to process handpicked datasets from raw files. This means that about 30% of datasets processed by Stemformatics fail the quality control metrics and never make it to the portal, ensuring that Stemformatics data are of high quality and have been processed in a consistent manner. Stemformatics provides easy-to-use and intuitive tools for biologists to visually explore the data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others. The addition of tools that facilitate cross-dataset comparisons provides users with snapshots of gene expression in multiple cell and tissues, assisting the identification of cell-type restricted genes, or potential housekeeping genes. Stemformatics is freely available at stemformatics.org. |
format | Online Article Text |
id | pubmed-6323943 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-63239432019-01-10 Stemformatics: visualize and download curated stem cell data Choi, Jarny Pacheco, Chris M Mosbergen, Rowland Korn, Othmar Chen, Tyrone Nagpal, Isha Englart, Steve Angel, Paul W Wells, Christine A Nucleic Acids Res Database Issue Stemformatics is an established gene expression data portal containing over 420 public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Developed for the stem cell community, it has a major focus on pluripotency, tissue stem cells, and staged differentiation. Stemformatics includes curated ‘collections’ of data relevant to cell reprogramming, as well as hematopoiesis and leukaemia. Rather than simply rehosting datasets as they appear in public repositories, Stemformatics uses a stringent set of quality control metrics and its own pipelines to process handpicked datasets from raw files. This means that about 30% of datasets processed by Stemformatics fail the quality control metrics and never make it to the portal, ensuring that Stemformatics data are of high quality and have been processed in a consistent manner. Stemformatics provides easy-to-use and intuitive tools for biologists to visually explore the data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others. The addition of tools that facilitate cross-dataset comparisons provides users with snapshots of gene expression in multiple cell and tissues, assisting the identification of cell-type restricted genes, or potential housekeeping genes. Stemformatics is freely available at stemformatics.org. Oxford University Press 2019-01-08 2018-11-08 /pmc/articles/PMC6323943/ /pubmed/30407577 http://dx.doi.org/10.1093/nar/gky1064 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. 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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Issue Choi, Jarny Pacheco, Chris M Mosbergen, Rowland Korn, Othmar Chen, Tyrone Nagpal, Isha Englart, Steve Angel, Paul W Wells, Christine A Stemformatics: visualize and download curated stem cell data |
title | Stemformatics: visualize and download curated stem cell data |
title_full | Stemformatics: visualize and download curated stem cell data |
title_fullStr | Stemformatics: visualize and download curated stem cell data |
title_full_unstemmed | Stemformatics: visualize and download curated stem cell data |
title_short | Stemformatics: visualize and download curated stem cell data |
title_sort | stemformatics: visualize and download curated stem cell data |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323943/ https://www.ncbi.nlm.nih.gov/pubmed/30407577 http://dx.doi.org/10.1093/nar/gky1064 |
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