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DNAmDeconv pipeline: Citations

DNAmDeconv

Add citation after paper is published.

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

  • meth_atlas

    Moss, J.; Magenheim, J.; Neiman, D.; Zemmour, H.; Loyfer, N.; Korach, A.; Samet, Y.; Maoz, M.; Druid, H.; Arner, P.; et al. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat. Commun. 2018, 9, 5068.

  • CIBERSORT

    Newman, A., Liu, C., Green, M. et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods 12, 453–457 (2015).

  • EpiDISH

    Teschendorff, A.E., Breeze, C.E., Zheng, S.C. et al. A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. BMC Bioinformatics 18, 105 (2017)

  • EpiSCORE

    Teschendorff, A.E., Zhu, T., Breeze, C.E. et al. EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data. Genome Biol 21, 221 (2020)

  • Methyl_Resolver

    Arneson, D., Yang, X. & Wang, K. MethylResolver—a method for deconvoluting bulk DNA methylation profiles into known and unknown cell contents. Commun Biol 3, 422 (2020)

  • PRMeth

    He, D., Chen, M., Wang, W. et al. Deconvolution of tumor composition using partially available DNA methylation data. BMC Bioinformatics 23, 355 (2022)

  • MeDeCom

    Lutsik, P., Slawski, M., Gasparoni, G. et al. MeDeCom: discovery and quantification of latent components of heterogeneous methylomes. Genome Biol 18, 55 (2017)

  • RefFreeCellMix

    Eugene Andres Houseman, John Molitor, Carmen J. Marsit, Reference-free cell mixture adjustments in analysis of DNA methylation data, Bioinformatics, Volume 30, Issue 10 (May 2014)

  • Houseman's CP

    Houseman, E.A., Accomando, W.P., Koestler, D.C. et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 13, 86 (2012).

  • CelFiE

    Caggiano, C., Celona, B., Garton, F. et al. Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE. Nat Commun 12, 2717 (2021)

  • MetDecode

    Antoine Passemiers, Stefania Tuveri, Dhanya Sudhakaran, Tatjana Jatsenko, Tina Laga, Kevin Punie, Sigrid Hatse, Sabine Tejpar, An Coosemans, Els Van Nieuwenhuysen, Dirk Timmerman, Giuseppe Floris, Anne-Sophie Van Rompuy, Xavier Sagaert, Antonia Testa, Daniela Ficherova, Daniele Raimondi, Frederic Amant, Liesbeth Lenaerts, Yves Moreau, Joris R Vermeesch, MetDecode: methylation-based deconvolution of cell-free DNA for noninvasive multi-cancer typing, Bioinformatics, Volume 40, Issue 9, September 2024, btae522.

  • limma

    Matthew E. Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W. Law, Wei Shi, Gordon K. Smyth, limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Research, Volume 43, Issue 7, 20 April 2015

  • BEDTools

    Aaron R. Quinlan, Ira M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, Volume 26, Issue 6, March 2010, Pages 841–842

Software packaging/containerisation tools

  • Docker

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

  • Singularity

    Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459