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ST Pipeline: an automated pipeline for spatial mapping of unique transcripts.
Navarro, José Fernández; Sjöstrand, Joel; Salmén, Fredrik; Lundeberg, Joakim; Ståhl, Patrik L.
Afiliación
  • Navarro JF; Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden.
  • Sjöstrand J; Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden.
  • Salmén F; Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden.
  • Lundeberg J; Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden.
  • Ståhl PL; Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden.
Bioinformatics ; 33(16): 2591-2593, 2017 Aug 15.
Article en En | MEDLINE | ID: mdl-28398467
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. AVAILABILITY AND IMPLEMENTATION: The ST Pipeline is open source under a MIT license and it is available at https://github.com/SpatialTranscriptomicsResearch/st_pipeline. CONTACT: jose.fernandez.navarro@scilifelab.se. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Análisis de Secuencia de ARN / Perfilación de la Expresión Génica / Análisis Espacial Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2017 Tipo del documento: Article País de afiliación: Suecia Pais de publicación: Reino Unido
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Análisis de Secuencia de ARN / Perfilación de la Expresión Génica / Análisis Espacial Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2017 Tipo del documento: Article País de afiliación: Suecia Pais de publicación: Reino Unido