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ST Pipeline: an automated pipeline for spatial mapping of unique transcripts
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
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2017 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 33, no 16, p. 2591-2593Article in journal (Refereed) Published
Abstract [en]

Motivation: In recent years we have witnessed an increase in novel RNA-seq based techniques for transcriptomics analysis. Spatial transcriptomics is a novel RNA-seq based technique that allows spatial mapping of transcripts in tissue sections. The spatial resolution adds an extra level of complexity, which requires the development of new tools and algorithms for efficient and accurate data processing. Results: Here we present a pipeline to automatically and efficiently process RNA-seq data obtained from spatial transcriptomics experiments to generate datasets for downstream analysis.

Place, publisher, year, edition, pages
Oxford University Press, 2017. Vol. 33, no 16, p. 2591-2593
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:kth:diva-212596DOI: 10.1093/bioinformatics/btx211ISI: 000407139800026OAI: oai:DiVA.org:kth-212596DiVA, id: diva2:1136056
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilSwedish Foundation for Strategic Research EU, Horizon 2020, 643417Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20170825

Available from: 2017-08-25 Created: 2017-08-25 Last updated: 2018-01-13Bibliographically approved

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Navarro, Jose FernandezSjöstrand, JoelSalmén, FredrikLundeberg, JoakimStåhl, Patrik L.
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Gene TechnologyScience for Life Laboratory, SciLifeLab
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Output format
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