How to cite GLINT?¶
If you use GLINT in any published work, please cite the paper describing it:
Rahmani, Elior, Reut Yedidim, Liat Shenhav, Regev Schweiger, Omer Weissbrod, Noah Zaitlen, and Eran Halperin. “GLINT: a user-friendly toolset for the analysis of high-throughput DNA-methylation array data.” Bioinformatics 2017; 33 (12): 1870-1872.
- If you use the –refactor argument please also cite:
Rahmani, Elior, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh et al. “Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.” Nature methods 13, no. 5 (2016): 443-445.
Rahmani, Elior, Liat Shenhav, Regev Schweiger, Paul Yousefi, Karen Huen, Brenda Eskenazi, Celeste Eng et al. “Genome-wide methylation data mirror ancestry information.” Epigenetics & Chromatin 10, 1 (2017).
Chen, Yi-an, Mathieu Lemire, Sanaa Choufani, Darci T. Butcher, Daria Grafodatskaya, Brent W. Zanke, Steven Gallinger, Thomas J. Hudson, and Rosanna Weksberg. “Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray.” Epigenetics 8, no. 2 (2013): 203-209.
- If you use the –rmns argument for 850K (EPIC) data please cite:
McCartney, Daniel L., Rosie M. Walker, Stewart W. Morris, Andrew M. McIntosh, David J. Porteous, and Kathryn L. Evans. “Identification of polymorphic and off-target probe binding sites on the Illumina Infinium MethylationEPIC BeadChip.” Genomics Data 9 (2016): 22-24.
- If you use the –lmm argument please also cite:
Lippert, Christoph, Jennifer Listgarten, Ying Liu, Carl M. Kadie, Robert I. Davidson, and David Heckerman. “FaST linear mixed models for genome-wide association studies.” Nature methods 8, no. 10 (2011): 833-835.
- If you use the –houseman argument please also cite:
Houseman, Eugene Andres, William P. Accomando, Devin C. Koestler, Brock C. Christensen, Carmen J. Marsit, Heather H. Nelson, John K. Wiencke, and Karl T. Kelsey. “DNA methylation arrays as surrogate measures of cell mixture distribution.” BMC bioinformatics 13, no. 1 (2012): 1.
and if you use the default reference data please also cite:
Reinius, Lovisa E., Nathalie Acevedo, Maaike Joerink, Göran Pershagen, Sven-Erik Dahlén, Dario Greco, Cilla Söderhäll, Annika Scheynius, and Juha Kere. “Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility.” PloS one 7, no. 7 (2012): e41361.
Koestler, Devin C., Meaghan J. Jones, Joseph Usset, Brock C. Christensen, Rondi A. Butler, Michael S. Kobor, John K. Wiencke, and Karl T. Kelsey. “Improving cell mixture deconvolution by id entifying o ptimal DNA methylation l ibraries (IDOL).” BMC bioinformatics 17, no. 1 (2016): 1.