ulfasQTL is a very efficient tool for composite splicing QTL analysis and can be applied on whole-genome analysis with acceptable time.doi:10.1186/s12864-016-3258-1Yang, QianHu, YueLi, JunZhang, XuegongBioMed CentralBMC Genomics
Published online 17 October 2018 Nucleic Acids Research, 2019, Vol. 47, Database issue D909–D916doi: 10.1093/nar/gky954CancerSplicingQTL: a database for genome-wideidentif i cation of splicing QTLs in human cancerJianbo Tian 1,† , Zhihua Wang 2,† , Shufang Mei 1 , Nan Yang 1...
devtools::install_github("jmonlong/sQTLseekeR") Or a specific release: devtools::install_github("jmonlong/sQTLseekeR", ref="2.1") All these installation commands are also written ininstall.Rscript (sourceit to install). These commands work for R 3.2 or higher. For R 3.1, some packages...
we performed a multitrait colocalization analysis to identify molecular QTLs that probably share causal variants (Fig.4a, Supplementary Fig.13aandMethods). For example, at theCCHRC1locus, we identify an eQTL, an hQTL and an sQTL (Fig.4a). While both the sQTL and hQTL are nominally signifi...
visualizationrna-seqstatisticsalternative-splicingballgownsplicingsqtl3s-scores UpdatedJan 7, 2022 R Load more… Add a description, image, and links to thesplicingtopic page so that developers can more easily learn about it. To associate your repository with thesplicingtopic, visit your repo's land...
(r2< 0.6) between the lead sQTL and exon-QTL variant for 45.2% of overlapping genes (Additional file1: Fig. S2d, e). This indicates that sQTLs, which directly measure splice junction variation, and exon-QTLs, which measure exon expression levels and can thus be influenced by variables ...
(Section 2 of theSupplementary Note) and focused on the comparison with sQTLseekeR. There was no inflation in false positive rate (FPR) under the null hypothesis of no sQTL effect for both THISTLE and sQTLseekeR, in either the absence or presence of an eQTL effect (Supplementary Fig.1)....
The vast majority of methods commonly used for sQTL mapping treat splicing as a univariate phenotype. They assess association between genetic variants and the abundance of individual transcripts7,16, or the splicing of individual exons9,17 or introns12,15. However, this approach ignores the strongl...
The numbers below the cell type labels indicate the sample size for differential splicing analysis and sQTL calling. f, Number of alternatively spliced genes detected per cell across 21 cell types at the single-cell level (see Supplementary Table 1 for the number of cells used (n)). The ...
We have evaluated three statistical methods for the analysis of sQTLs in RNA-Seq. Results from our study will be instructive for researchers in selecting the appropriate statistical methods for sQTL analysis. 展开 关键词: alternative splicing quantitative trait loci RNA-Seq ...