Treeqtl

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August undefined, 2024

WebMatrix eQTL: ultra fast eQTL analysis via large matrix operations. Motivation: Expression quantitative trait loci (eQTL) analysis links variations in gene expression levels to genotypes. For modern datasets, eQTL analysis is a computationally intensive task as it involves testing for association of billions of transcript-SNP (single-nucleotide ... WebMay 20, 2024 · TreeQTL uses a hierarchical FDR correction procedure, which performs FDR correction first on the gene level, and then on the association level (gene by SNP). We used FDR < 0.05 on both gene and ...

TreeQTL 2.0 – Hierarchical error control for eQTL studies

WebSep 5, 2024 · Recently, hierarchical procedures, such as TreeQTL , have been proposed, which first control for multiple testing of variants at each gene, before controlling for multiple testing across all genes. Taken together, with many correction methods available, ... Webi10-index. 50. 48. Follow. Christine B. Peterson. Associate Professor of Biostatistics, University of Texas MD Anderson Cancer Center. Verified email at mdanderson.org - Homepage. graphical models variable selection Bayesian statistics microbiome data. pep boys hydraulic oil

TreeQTL: hierarchical error control for eQTL findings bioRxiv

WebAnything in here will be replaced on browsers that support the canvas element WebIn the top 25% of all research outputs scored by Altmetric WebMar 16, 2024 · Background Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction … tom arnold bill paxton

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Treeqtl

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WebMay 11, 2024 · Background With the rapid development of single-cell genomics, technologies for parallel sequencing of the transcriptome and genome in each single cell is being explored in several labs and is becoming available. This brings us the opportunity to uncover association between genotypes and gene expression phenotypes at single-cell … WebJul 7, 2015 · Summary Commonly used multiplicity adjustments fail to control the error rate for reported findings in many expression quantitative trait loci (eQTL) studies. TreeQTL ...

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WebMay 15, 2024 · Posted on 2024/05/15 Author admin Categories Genetics & Pedigree Tags eQTL, Hierarchical error, TreeQTL Leave a Reply Cancel reply Your email address will not … WebDec 18, 2024 · Abstract. We present the R-package GenomicTools that can be used to perform QTL and eQTL analyses in a user-friendly way. First, the theoretical backgrounds of both implemented methods are explained. These are (a) the linear model approach that is commonly used in the standard QTL/eQTL testing as well as (b) a non-parametrical …

WebInstead, we used TreeQTL tosimultaneously controlforSNP-levelFDRandgene-levelFDR.38 Note that TreeQTL is more conservative than permutation. 378 The American Journal of Human Genetics 103, 377–388, September 6, 2024. Quantifying Tissue- and Cell Type-Speciﬁc Contribution WebNov 4, 2024 · While an individual’s genome sequence is mostly stable throughout life, gene expression and genetic regulation of expression fluctuate in response to different environmental exposures [1–3].The impact of aging on gene expression and genetic regulation has been well-studied in model systems, such as yeast, fruit fly, or worm [4, 5], …

WebChristine B. Peterson, PhD DepartmentofBiostatistics E-mail: [email protected] UniversityofTexasMDAndersonCancerCenter Phone: 713-563-7560 WebTel Aviv University Home. Request a data update (TAU staff only)

WebMethods for multiple-testing correction in local expression quantitative trait locus (cis-eQTL) studies are a trade-off between statistical power and computational efficiency. Bonferroni correction, though computationally trivial, is overly conservative and fails to account for linkage disequilibrium between variants. Permutation-based methods are more powerful, …

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