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nf-core/imcyto: Citations

nf-core

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

Nextflow

Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

Pipeline tools

  • CellProfiler

    McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE. CellProfiler 3.0: Next-generation image processing for biology. PLoS Biol. 2018 Jul 3;16(7):e2005970. doi: 10.1371/journal.pbio.2005970. eCollection 2018 Jul. PubMed PMID: 29969450; PubMed Central PMCID: PMC6029841.

  • ilastik

    Berg S, Kutra D, Kroeger T, Straehle CN, Kausler BX, Haubold C, Schiegg M, Ales J, Beier T, Rudy M, Eren K, Cervantes JI, Xu B, Beuttenmueller F, Wolny A, Zhang C, Koethe U, Hamprecht FA, Kreshuk A. ilastik: interactive machine learning for (bio)image analysis. Nat Methods. 2019 Sep 30. doi: 10.1038/s41592-019-0582-9. [Epub ahead of print] Review. PubMed PMID: 31570887.

  • histoCAT

    Schapiro D, Jackson HW, Raghuraman S, Fischer JR, Zanotelli VRT, Schulz D, Giesen C, Catena R, Varga Z, Bodenmiller B. histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data. Nat Methods. 2017 Sep;14(9):873-876. doi: 10.1038/nmeth.4391. Epub 2017 Aug 7. PubMed PMID: 28783155; PubMed Central PMCID: PMC5617107.

  • imctools

  • Zanotelli & Bodenmiller, Jan 2019

  • CellProfiler Bodenmiller custom plugins

Software packaging/containerisation tools

  • BioContainers

    da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

  • Singularity

    Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

  • Docker