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ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0003-4313-1601
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
2019 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 35, no 6, p. 1058-1060Article in journal (Refereed) Published
Abstract [en]

Motivation Spatial Transcriptomics (ST) is a technique that combines high-resolution imaging with spatially resolved transcriptome-wide sequencing. This novel type of data opens up many possibilities for analysis and visualization, most of which are either not available with standard tools or too complex for normal users. Results Here, we present a tool, ST Viewer, which allows real-time interaction, analysis and visualization of Spatial Transcriptomics datasets through a seamless and smooth user interface. Availability and implementation The ST Viewer is open source under a MIT license and it is available at https://github.com/SpatialTranscriptomicsResearch/st_viewer. Supplementary information Supplementary data are available at Bioinformatics online.

Place, publisher, year, edition, pages
Oxford University Press, 2019. Vol. 35, no 6, p. 1058-1060
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-249886DOI: 10.1093/bioinformatics/bty714ISI: 000462709200023PubMedID: 30875427Scopus ID: 2-s2.0-85063013580OAI: oai:DiVA.org:kth-249886DiVA, id: diva2:1306728
Note

QC 20190424

Available from: 2019-04-24 Created: 2019-04-24 Last updated: 2019-04-24Bibliographically approved

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Fernandez Navarro, JoseLundeberg, Joakim

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