# nf-core/nanostring: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> 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](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> 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

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
  > 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.
- [NACHO](https://pubmed.ncbi.nlm.nih.gov/31504159/)
  > Canouil M, Bouland GA, Bonnefond A, Froguel P, Hart L, Slieker R. NACHO: an R package for quality control of NanoString nCounter data. Bioinformatics. 2019 Aug 23;36(3), 970-971. doi: 10.1093/bioinformatics/btz647. PubMed PMID: 31504159; PubMed Central PMCID: PMC9883715.
- [GSVA](https://link.springer.com/article/10.1186/1471-2105-14-7)
  > Hänzelmann, Sonja, Robert Castelo, and Justin Guinney. "GSVA: gene set variation analysis for microarray and RNA-seq data." BMC bioinformatics 14 (2013): 1-15.
- [SINGSCORE](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2435-4)
  > Foroutan, M., Bhuva, D.D., Lyu, R. et al. Single sample scoring of molecular phenotypes. BMC Bioinformatics 19, 404 (2018)
- [PLAGE](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-225)
  > Tomfohr J, Lu J, Kepler TB. Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics. 2005;6:225.
- [SSGSEA] (see GSVA)
- [SAMS](https://www.pnas.org/doi/abs/10.1073/pnas.091062498)
  > Tusher, Virginia Goss, Robert Tibshirani, and Gilbert Chu. "Significance analysis of microarrays applied to the ionizing radiation response." Proceedings of the National Academy of Sciences 98.9 (2001): 5116-5121.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

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

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > 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](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > 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](https://dl.acm.org/doi/10.5555/2600239.2600241)

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

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > 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.
