MatrixEQTL: Matrix eQTL: Ultra fast eQTL analysis via large matrix operations

Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for association between genotype and gene expression using linear regression with either additive or ANOVA genotype effects. The models can include covariates to account for factors as population stratification, gender, and clinical variables. It also supports models with heteroscedastic and/or correlated errors, false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs.

AuthorAndrey Shabalin
Date of publication2015-02-03 06:53:36
MaintainerAndrey Shabalin <ashabalin@vcu.edu>
LicenseLGPL-3
Version2.1.1
http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

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Files in this package

MatrixEQTL
MatrixEQTL/inst
MatrixEQTL/inst/CITATION
MatrixEQTL/NAMESPACE
MatrixEQTL/demo
MatrixEQTL/demo/e.interaction.r
MatrixEQTL/demo/d.ANOVA5.r
MatrixEQTL/demo/c.weights.r
MatrixEQTL/demo/sample.cis.r
MatrixEQTL/demo/sample.all.r
MatrixEQTL/demo/d.ANOVA.r
MatrixEQTL/demo/00Index
MatrixEQTL/demo/a.nocvrt.r
MatrixEQTL/demo/q.qqplot.r
MatrixEQTL/demo/b.cvrt.r
MatrixEQTL/demo/p.hist.r
MatrixEQTL/data
MatrixEQTL/data/GE.txt
MatrixEQTL/data/snpsloc.txt
MatrixEQTL/data/SNP.txt
MatrixEQTL/data/Covariates.txt
MatrixEQTL/data/geneloc.txt
MatrixEQTL/R
MatrixEQTL/R/Matrix_eQTL_engine.R
MatrixEQTL/MD5
MatrixEQTL/DESCRIPTION
MatrixEQTL/man
MatrixEQTL/man/Covariates.Rd
MatrixEQTL/man/figures
MatrixEQTL/man/figures/QQplot.png
MatrixEQTL/man/figures/histogram.png
MatrixEQTL/man/plot.MatrixEQTL.Rd MatrixEQTL/man/modelLINEAR.Rd MatrixEQTL/man/MatrixEQTL_cis_code.Rd MatrixEQTL/man/geneloc.Rd MatrixEQTL/man/Matrix_eQTL_main.Rd MatrixEQTL/man/MatrixEQTL-package.Rd MatrixEQTL/man/SlicedData-class.Rd MatrixEQTL/man/modelANOVA.Rd MatrixEQTL/man/SNP.Rd MatrixEQTL/man/modelLINEAR_CROSS.Rd MatrixEQTL/man/GE.Rd MatrixEQTL/man/snpsloc.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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