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2
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BMC Bioinformatics. 2017 Feb 13;18(1):105. doi: 10.1186/s12859-017-1511-5.
3
Reference-free deconvolution of DNA methylation data and mediation by cell composition effects.
BMC Bioinformatics. 2016 Jun 29;17:259. doi: 10.1186/s12859-016-1140-4.
4
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Mol Cell. 2016 Apr 21;62(2):157-168. doi: 10.1016/j.molcel.2016.03.019.
5
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PLoS Genet. 2015 May 8;11(5):e1005223. doi: 10.1371/journal.pgen.1005223. eCollection 2015 May.
6
Robust enumeration of cell subsets from tissue expression profiles.
Nat Methods. 2015 May;12(5):453-7. doi: 10.1038/nmeth.3337. Epub 2015 Mar 30.
7
limma powers differential expression analyses for RNA-sequencing and microarray studies.
Nucleic Acids Res. 2015 Apr 20;43(7):e47. doi: 10.1093/nar/gkv007. Epub 2015 Jan 20.
8
A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data.
Nucleic Acids Res. 2014 Apr;42(8):e69. doi: 10.1093/nar/gku154. Epub 2014 Feb 22.
9
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