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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...

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Autores principales: Choi, Jarny, Pacheco, Chris M, Mosbergen, Rowland, Korn, Othmar, Chen, Tyrone, Nagpal, Isha, Englart, Steve, Angel, Paul W, Wells, Christine A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
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.
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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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