{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T23:02:43Z","timestamp":1762642963114,"version":"3.41.2"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T00:00:00Z","timestamp":1705017600000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Boehringer Ingelheim Pharma GmbH & Co"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The NanoString\u2122 nCounter\u00ae technology platform is a widely used targeted quantification platform for the analysis of gene expression of up to \u223c800 genes. Whereas the software tools by the manufacturer can perform the analysis in an interactive and GUI driven approach, there is no portable and user-friendly workflow available that can be used to perform reproducible analysis of multiple samples simultaneously in a scalable fashion on different computing infrastructures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present the nf-core\/nanostring open-source pipeline to perform a comprehensive analysis including quality control and additional features such as expression visualization, annotation with additional metadata and input creation for differential gene expression analysis. The workflow features an easy installation, comprehensive documentation, open-source code with the possibility for further extensions, a strong portability across multiple computing environments and detailed quality metrics reporting covering all parts of the pipeline. nf-core\/nanostring has been implemented in the Nextflow workflow language and supports Docker, Singularity, Podman container technologies as well as Conda environments, enabling easy deployment on any Nextflow supported compatible system, including most widely used cloud computing environments such as Google GCP or Amazon AWS.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code, documentation and installation instructions as well as results for continuous tests are freely available at https:\/\/github.com\/nf-core\/nanostring and https:\/\/nf-co.re\/nanostring.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae019","type":"journal-article","created":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T06:05:12Z","timestamp":1705039512000},"source":"Crossref","is-referenced-by-count":3,"title":["nf-core\/nanostring: a pipeline for reproducible NanoString nCounter analysis"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6503-2180","authenticated-orcid":false,"given":"Alexander","family":"Peltzer","sequence":"first","affiliation":[{"name":"Clinical Bioinformatics and Systems Pharmacology, Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG , 88400 Biberach\/Riss, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher","family":"Mohr","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics and Systems Pharmacology, Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG , 88400 Biberach\/Riss, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8036-1492","authenticated-orcid":false,"given":"Kai B","family":"Stadermann","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics and Systems Pharmacology, Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG , 88400 Biberach\/Riss, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthias","family":"Zwick","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics and Systems Pharmacology, Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG , 88400 Biberach\/Riss, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramona","family":"Schmid","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics and Systems Pharmacology, Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. 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