ArticleBioinformatics (Oxford, England)2023
mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- From association to causation: a decision-aware framework for reproducible biomarker discovery and precision intervention design in the human gut microbiome.Briefings in bioinformatics · 2026Article
- Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.International journal of molecular sciences · 2025Review
- Causal associations between the gut microbiota and multiple myeloma: a two-sample Mendelian randomization study.Frontiers in nutrition · 2024Article
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Authors and funding
3 authors.
Funding
Abstract
motivationIn recent years, significant strides have been made in the field of genomics, with the commencement of large-scale studies aimed at collecting host mutational profiles and microbiome data. The amalgamation of host gene mutational profiles in both healthy and diseased subjects with microbial abundance data holds immense promise in providing insights into several crucial research questions, including the development and progression of diseases, as well as individual responses to therapeutic interventions. With the advent of sequencing methods such as 16s ribosomal RNA (rRNA) sequencing and whole genome sequencing, there is increasing evidence of interplay of human genetics and microbial communities. Quantitative trait loci associated with microbial abundance (mbQTLs), are genetic variants that influence the abundance of microbial populations within the host.
resultsHere, we introduce mbQTL, the first R package integrating 16S ribosomal RNA (rRNA) sequencing and single-nucleotide variation (SNV) and single-nucleotide polymorphism (SNP) data. We describe various statistical methods implemented for the identification of microbe-SNV pairs, relevant statistical measures, and plot functionality for interpretation. AVAILABILITY AND IMPLEMENTATION: mbQTL is available on bioconductor at https://bioconductor.org/packages/mbQTL/.
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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 OpenQuestion graph.