Skip to content

Latest commit

 

History

History
97 lines (55 loc) · 5.43 KB

CITATIONS.md

File metadata and controls

97 lines (55 loc) · 5.43 KB
Raw

FluWarnSystem: Citations

VOCAL: Variant Of Concern ALert and prioritization

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

  • Nextclade

    Aksamentov, I., Roemer, C., Hodcroft, E. B., & Neher, R. A., (2021). Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software, 6(67), 3773, https://doi.org/10.21105/joss.03773

The customized scripts in bin use the following languages and packages:

Python

  • BioPython

    Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423

  • NumPy

    Harris CR, Millman KJ, van der Walt SJ et al. Array programming with NumPy. Nature 585, 357–362 (2020). DOI: 10.1038/s41586-020-2649-2.

  • Pandas

  • argparse

  • itertools

  • operator

  • sys

  • time

  • typing

  • warnings

R

R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

  • rmarkdown

    Xie Y, Allaire J, Grolemund G (2018). R Markdown: The Definitive Guide. Chapman and Hall/CRC, Boca Raton, Florida. ISBN 9781138359338, https://bookdown.org/yihui/rmarkdown.

    Xie Y, Dervieux C, Riederer E (2020). R Markdown Cookbook. Chapman and Hall/CRC, Boca Raton, Florida. ISBN 9780367563837, https://bookdown.org/yihui/rmarkdown-cookbook.

    Allaire J, Xie Y, Dervieux C, McPherson J, Luraschi J, Ushey K, Atkins A, Wickham H, Cheng J, Chang W, Iannone R (2023). rmarkdown: Dynamic Documents for R. R package version 2.25, https://github.com/rstudio/rmarkdown.

  • optparse

  • dplyr

  • tidyr

  • readr

  • stringr

  • purrr

  • igraph

    Csardi G, Nepusz T (2006). “The igraph software package for complex network research.” InterJournal, Complex Systems, 1695. https://igraph.org.

    Csárdi G, Nepusz T, Traag V, Horvát S, Zanini F, Noom D, Müller K (2023). igraph: Network Analysis and Visualization in R. doi:10.5281/zenodo.7682609, R package version 1.6.0.

  • forcats

  • logger

  • tidyverse

    Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). “Welcome to the tidyverse.” Journal of Open Source Software, 4(43), 1686. doi:10.21105/joss.01686.

  • stringi

    Gagolewski M (2022). “stringi: Fast and portable character string processing in R.” Journal of Statistical Software, 103(2), 1–59. doi:10.18637/jss.v103.i02.

  • readxl

  • seqinr

    Charif D, Lobry J (2007). “SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis.” In Bastolla U, Porto M, Roman H, Vendruscolo M (eds.), Structural approaches to sequence evolution: Molecules, networks, populations, series Biological and Medical Physics, Biomedical Engineering, 207-232. Springer Verlag, New York. ISBN : 978-3-540-35305-8.

  • ggplot2

    Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org.

  • plotly

    Sievert C (2020). Interactive Web-Based Data Visualization with R, plotly, and shiny. Chapman and Hall/CRC. ISBN 9781138331457, https://plotly-r.com.

  • DT

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.