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dc.contributor.authorChoi, J
dc.contributor.authorPacheco, CM
dc.contributor.authorMosbergen, R
dc.contributor.authorKorn, O
dc.contributor.authorChen, T
dc.contributor.authorNagpal, I
dc.contributor.authorEnglart, S
dc.contributor.authorAngel, PW
dc.contributor.authorWells, CA
dc.date.accessioned2020-12-09T23:02:18Z
dc.date.available2020-12-09T23:02:18Z
dc.date.issued2019-01-08
dc.identifierpii: 5165343
dc.identifier.citationChoi, J., Pacheco, C. M., Mosbergen, R., Korn, O., Chen, T., Nagpal, I., Englart, S., Angel, P. W. & Wells, C. A. (2019). Stemformatics: visualize and download curated stem cell data. NUCLEIC ACIDS RESEARCH, 47 (D1), pp.D841-D846. https://doi.org/10.1093/nar/gky1064.
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/11343/253124
dc.description.abstractStemformatics 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.
dc.languageEnglish
dc.publisherOXFORD UNIV PRESS
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleStemformatics: visualize and download curated stem cell data
dc.typeJournal Article
dc.identifier.doi10.1093/nar/gky1064
melbourne.affiliation.departmentAnatomy and Neuroscience
melbourne.affiliation.departmentSchool of Historical and Philosophical Studies
melbourne.source.titleNucleic Acids Research
melbourne.source.volume47
melbourne.source.issueD1
melbourne.source.pagesD841-D846
melbourne.identifier.arcFT150100330
dc.rights.licenseCC BY
melbourne.elementsid1355589
melbourne.contributor.authorChoi, Jarny
melbourne.contributor.authorMosbergen, Rowland
melbourne.contributor.authorNagpal, Isha
melbourne.contributor.authorChen, Tyrone
melbourne.contributor.authorWells, Christine
melbourne.contributor.authorAngel, Paul
melbourne.contributor.authorEnglart, Steven
dc.identifier.eissn1362-4962
melbourne.identifier.fundernameidAustralian Research Council, FT150100330
melbourne.accessrightsOpen Access


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