ArticleBMC bioinformatics2021
A pipeline for RNA-seq based eQTL analysis with automated quality control procedures.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Pleiotropy and Facilitation of Local Adaptation in the Silverleaf Sunflower Helianthus argophyllus.Genome biology and evolution · 2026Article
- Genetic Architecture of Immune Cell DNA Methylation in the Rhesus Macaque.Molecular ecology · 2025Article
- Genetic transcriptional regulation profiling of cartilage reveals pathogenesis of osteoarthritis.EBioMedicine · 2025Article
- Neonatal Encephalopathy: Novel Phenotypes and Genotypes Identified by Genome Sequencing.Neurology. Genetics · 2025Article
- Widespread transposable element dysregulation in human aging brains with Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Article
- A brief guide to analyzing expression quantitative trait loci.Molecules and cells · 2024Review
- eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts.NAR genomics and bioinformatics · 2024Article
- The relationship between extreme inter-individual variation in macrophage gene expression and genetic susceptibility to inflammatory bowel disease.Human genetics · 2024Article
- A landscape of gene expression regulation for synovium in arthritis.Nature communications · 2024Article
- An integrative pipeline for circular RNA quantitative trait locus discovery with application in human T cells.Bioinformatics (Oxford, England) · 2023Article
- Affordable, accurate and unbiased RNA sequencing by manual library miniaturization: A case study in barley.Plant biotechnology journal · 2023Article
- BBmix: a Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing.Bioinformatics (Oxford, England) · 2023Article
- DEEMD-SPP: A Novel Framework for Emotion Recognition Based on EEG Signals.Frontiers in psychiatry · 2022Article
- Label-free Quantitative Proteomic Analysis of Cerebrospinal Fluid and Serum in Patients With Relapse-Remitting Multiple Sclerosis.Frontiers in genetics · 2022Article
- GARCOM: A user-friendly R package for genetic mutation counts.F1000Research · 2021Article
- Graph Embedding Based Novel Gene Discovery Associated With Diabetes Mellitus.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundAdvances in the expression quantitative trait loci (eQTL) studies have provided valuable insights into the mechanism of diseases and traits-associated genetic variants. However, it remains challenging to evaluate and control the quality of multi-source heterogeneous eQTL raw data for researchers with limited computational background. There is an urgent need to develop a powerful and user-friendly tool to automatically process the raw datasets in various formats and perform the eQTL mapping afterward.
resultsIn this work, we present a pipeline for eQTL analysis, termed eQTLQC, featured with automated data preprocessing for both genotype data and gene expression data. Our pipeline provides a set of quality control and normalization approaches, and utilizes automated techniques to reduce manual intervention. We demonstrate the utility and robustness of this pipeline by performing eQTL case studies using multiple independent real-world datasets with RNA-seq data and whole genome sequencing (WGS) based genotype data.
conclusionseQTLQC provides a reliable computational workflow for eQTL analysis. It provides standard quality control and normalization as well as eQTL mapping procedures for eQTL raw data in multiple formats. The source code, demo data, and instructions are freely available at https://github.com/stormlovetao/eQTLQC .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.