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nf-core/drugresponseeval: Citations

DrugResponseEval

Bernett, J, Iversen, P, Picciani, M, Wilhelm, M, Baum, K, List, M. Will be published soon.

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

  • DrEvalPy: The pipeline mostly automates the individual steps of the DrEvalPy PyPI package.

    Bernett, J, Iversen, P, Picciani, M, Wilhelm, M, Baum, K, List, M. Will be published soon.

  • DIPK: Implemented model in the pipeline.

    Li P, Jiang Z, Liu T, Liu X, Qiao H, Yao X. Improving drug response prediction via integrating gene relationships with deep learning. Briefings in Bioinformatics. 2024 May;25(3):bbae153.

  • MOLI: Implemented model in the pipeline.

    Sharifi-Noghabi H, Zolotareva O, Collins CC, Ester M. MOLI: multi-omics late integration with deep neural networks for drug response prediction. Bioinformatics. 2019 Jul;35(14):i501-9.

  • SRMF: Implemented model in the pipeline.

    Wang L, Li X, Zhang L, Gao Q. Improved anticancer drug response prediction in cell lines using matrix factorization with similarity regularization. BMC cancer. 2017 Dec;17:1-2.

  • SuperFELT: Implemented model in the pipeline.

    Park S, Soh J, Lee H. Super. FELT: supervised feature extraction learning using triplet loss for drug response prediction with multi-omics data. BMC bioinformatics. 2021 May 25;22(1):269.

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.