Anatomy and Neuroscience - Research Publications

Permanent URI for this collection

http://hdl.handle.net/11343/181

Filters

2019 1
1
Reset filters

Settings
Statistics
Citations
Author: Wells, Christine × Author: Choi, Jarny × Author: Chen, Tyrone × Author: Englart, Steven ×

Search Results

Now showing 1 - 1 of 1
  • Item
    Thumbnail Image
    Stemformatics: visualize and download curated stem cell data
    Choi, J ; Pacheco, CM ; Mosbergen, R ; Korn, O ; Chen, T ; Nagpal, I ; Englart, S ; Angel, PW ; Wells, CA (OXFORD UNIV PRESS, 2019-01-08)
    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.