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nf-core/spatialvi: 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

  • AnnData

    Virshup I, Rybakov S, Theis FJ, Angerer P, Wolf FA. bioRxiv 2021.12.16.473007; doi: https://doi.org/10.1101/2021.12.16.473007

  • FastQC

    Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

  • MultiQC

    Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

  • Quarto

    Allaire J, Teague C, Scheidegger C, Xie Y, Dervieux C. Quarto (2022). doi: 10.5281/zenodo.5960048

  • Scanpy

    Wolf F, Angerer P, Theis F. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol 19, 15 (2018). doi: https://doi.org/10.1186/s13059-017-1382-0

  • Space Ranger

    10x Genomics Space Ranger 2.1.0 [Online]

  • SpatialData

    Marconato L, Palla G, Yamauchi K, Virshup I, Heidari E, Treis T, Toth M, Shrestha R, Vöhringer H, Huber W, Gerstung M, Moore J, Theis F, Stegle O. SpatialData: an open and universal data framework for spatial omics. bioRxiv 2023.05.05.539647; doi: https://doi.org/10.1101/2023.05.05.539647

  • Squipy

    Palla G, Spitzer H, Klein M et al. Squidpy: a scalable framework for spatial omics analysis. Nat Methods 19, 171–178 (2022). doi: https://doi.org/10.1038/s41592-021-01358-2

Software packaging/containerisation tools

  • Anaconda

    Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

  • Bioconda

    Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

  • BioContainers

    da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, 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.

  • Docker

    Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

  • 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.