Cite nf-encyclopedia

nf-encyclopedia

TODO: Add preprint

Pipeline Tools:

MSconvert

Chambers, M. C., Maclean, B., Burke, R., Amodei, D., Ruderman, D. L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T. A., Brusniak, M.-Y., Paulse, C., Creasy, D., … Mallick, P. (2012). A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology, 30(10), 918–920. https://doi.org/10.1038/nbt.2377

EncyclopeDIA

Searle, B. C., Pino, L. K., Egertson, J. D., Ting, Y. S., Lawrence, R. T., MacLean, B. X., Villen, J., & MacCoss, M. J. (2018). Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-07454-w

MSstats

Choi, M., Chang, C.-Y., Clough, T., Broudy, D., Killeen, T., MacLean, B., & Vitek, O. (2014). MSstats: An R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics (Oxford, England), 30(17), 2524–2526. https://doi.org/10.1093/bioinformatics/btu305

Infrastructure:

Nextflow

Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. https://doi.org/10.1038/nbt.3820

nf-core

Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276–278. https://doi.org/10.1038/s41587-020-0439-x