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sQTLseekeR specifications


Unique identifier OMICS_11336
Name sQTLseekeR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Roderic Guigo

Publication for sQTLseekeR

sQTLseekeR citations


Identification of Splicing Quantitative Trait Loci (sQTL) in Drosophila melanogaster with Developmental Lead (Pb2+) Exposure

Front Genet
PMCID: 5660682
PMID: 29114259
DOI: 10.3389/fgene.2017.00145

[…] Gymrek, ; Kurmangaliyev et al., ); (4) use the fraction of reads in a gene that falls in a given exon as the phenotype (Figure ; Pickrell et al., ; Gymrek, ); and (5) multivariate approaches, such as sQTLseekeR (Gymrek, ; Monlong et al., ). The sQTLseekeR is a multivariate model called for each gene consisting of the relative abundance of each transcript (Monlong et al., ). It calculated the varia […]


Network directed cis mediator analysis of normal prostate tissue expression profiles reveals downstream regulatory associations of prostate cancer susceptibility loci

PMCID: 5689655
PMID: 29156765
DOI: 10.18632/oncotarget.20717

[…] of tumor and normal prostate tissues []. To explore whether significant eQTL SNPs corresponded to differential isoform usage, we conducted supplementary isoform-ratio QTL analyses using the R package sQTLSeeker [] and isoform abundances derived from StringTie v1.2.4 []. We identified one intronic SNP, rs3110641, to be associated with differential isoform expression (P = 2.0E-04), although this SNP […]


Evidence of selection on splicing associated loci in human populations and relevance to disease loci mapping

Sci Rep
PMCID: 5519721
PMID: 28729732
DOI: 10.1038/s41598-017-05744-9

[…] the possibility of splicing-specific regulatory function. Interestingly, rs4506565 (but not rs7901695) shows a nominally significant effect on transcript relative expression of TCF7L2 (p = 0.04) from sQTLseekeR first-phase GTEx data, although clearly this requires additional functional validation. […]


Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

PMCID: 5119954
PMID: 27863251
DOI: 10.1016/j.cell.2016.10.026

[…] or monocytes, neutrophils and naive CD4+ T cells. Abundance was reported in FPKM (expected fragments per kilobase of transcript per million fragments sequenced). For ISO sQTL mapping, we employed the sQTLseekeR R package (v2.0) (). sQTLseekeR provides an appropriate method to identify SNPs associated with the variation in the relative abundance of a gene’s transcript isoforms, or transcript ratios […]


Natural selection on HFE in Asian populations contributes to enhanced non heme iron absorption

BMC Genet
PMCID: 4460683
PMID: 26054392
DOI: 10.1186/s12863-015-0223-y

[…] rformed on the GTEx Portal (http://www.gtexportal.org/) in all tissues or cells available. The splicing effect of rs9366637 on the relative expression of different HFE transcripts was tested with the sQTLseekeR method in 9 tissues (adipose, blood, blood vessel, heart, lung, muscle, nerve, skin and thyroid) from the GTEx Project []. […]


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sQTLseekeR institution(s)
Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain; Department of Human Genetics, McGill University, Montréal, Canada; Department of Statistics, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; Institute for Genetics and Genomics in Geneva (G3), University of Geneva, Geneva, Switzerland; Swiss Institute of Bioinformatics, Geneva, Switzerland; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
sQTLseekeR funding source(s)
This work was supported by grant 1R01MH090941-01 and R01MH101814 from the US National Institutes of Health, and grants BIO2011-26205 and CSD2007-00050 from the Ministerio de Educación y Ciencia (Spain) and grant ERC_294653 from the European Research Council.

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