├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── MatrixEQTL.Rproj ├── NAMESPACE ├── R └── Matrix_eQTL_engine.R ├── README.md ├── data ├── Covariates.txt ├── GE.txt ├── SNP.txt ├── geneloc.txt └── snpsloc.txt ├── demo ├── 00Index ├── a.nocvrt.r ├── b.cvrt.r ├── c.weights.r ├── d.ANOVA.r ├── e.ANOVA5.r ├── f.interaction.r ├── p.hist.r ├── q.qqplot.r ├── sample.all.r └── sample.cis.r ├── inst └── CITATION ├── man ├── Covariates.Rd ├── GE.Rd ├── MatrixEQTL-package.Rd ├── MatrixEQTL_cis_code.Rd ├── Matrix_eQTL_main.Rd ├── SNP.Rd ├── SlicedData-class.Rd ├── figures │ ├── QQplot.png │ └── histogram.png ├── geneloc.Rd ├── modelANOVA.Rd ├── modelLINEAR.Rd ├── modelLINEAR_CROSS.Rd ├── plot.MatrixEQTL.Rd └── snpsloc.Rd └── website └── external.png /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andreyshabalin/MatrixEQTL/HEAD/.Rbuildignore 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