Matrix eQTL protocols

Matrix eQTL specifications

Information


Unique identifier OMICS_04606
Name Matrix eQTL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.1.0
Stability Stable
Maintained Yes

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Publication for Matrix eQTL

Matrix eQTL IN pipelines

 (2)
2016
PMCID: 4807760
PMID: 27015273
DOI: 10.1371/journal.pone.0152425

[…] for each gene. before eqtl analysis, expression quantifications were normalized by peer correction [9] and transformed into standard normal distribution. eqtls were mapped using a linear model in matrix eqtl [10] and permutations were used for fdr estimation., for fcγr genes with updated refseq annotation, the number of reads uniquely mapped to each gene in each sample was counted using htseq […]

2016
PMCID: 5094714
PMID: 27812116
DOI: 10.1371/journal.pgen.1006407

[…] analysis. for each polymorphic position, the samples were divided into groups according to their allele assignment. as described in lappalainen [26] et al., using the linear model implemented in the matrix eqtl r package [43], eqtl mapping was calculated according to the allele assignment, while considering gender, mtdna copy number and sample resource (i.e. lab of origin) as covariates. […]

Matrix eQTL institution(s)
Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

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