ArticleBMC bioinformatics2021
tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R.
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 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed.
- Genome-wide analysis of flax bZIP genes using a T2T genome reveals abiotic stress roles.iScience · 2026Article
- Identification of PP2C gene family and its role in stress and adversity based on T2T flax (Linum usitatissimum L.) genome.BMC plant biology · 2025Article
- Identification and Characterization of WOX Gene Family in Flax (International journal of molecular sciences · 2025Article
- Article
- Coix Seed Oil Alleviates DSS-Induced Ulcerative Colitis via Intestinal Barrier Repair and Ferroptosis Regulation.Journal of inflammation research · 2025Article
- Article
- Construction of a gene model related to the prognosis of patients with gastric cancer receiving immunotherapy and exploration of COX7A1 gene function.European journal of medical research · 2024Article
- Genome-Wide Analysis of Flax (International journal of molecular sciences · 2023Article
- Global Transcriptomic Analyses Provide New Insight into the Molecular Mechanisms of Endocarp Formation and Development in Iron Walnut (International journal of molecular sciences · 2023Article
- Gut Microbiome Remains Static in Functional Abdominal Pain Disorders Patients Compared to Controls: Potential for Diagnostic Tools.Biotech (Basel (Switzerland)) · 2022Article
- Exploring the Microbiome Analysis and Visualization Landscape.Frontiers in bioinformatics · 2021Review
- Gestational Diabetes Is Uniquely Associated With Altered Early Seeding of the Infant Gut Microbiota.Frontiers in endocrinology · 2020Article
- An exercise intervention alters stool microbiota and metabolites among older, sedentary adults.Therapeutic advances in infectious diseaseArticle
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundThe drive to understand how microbial communities interact with their environments has inspired innovations across many fields. The data generated from sequence-based analyses of microbial communities typically are of high dimensionality and can involve multiple data tables consisting of taxonomic or functional gene/pathway counts. Merging multiple high dimensional tables with study-related metadata can be challenging. Existing microbiome pipelines available in R have created their own data structures to manage this problem. However, these data structures may be unfamiliar to analysts new to microbiome data or R and do not allow for deviations from internal workflows. Existing analysis tools also focus primarily on community-level analyses and exploratory visualizations, as opposed to analyses of individual taxa.
resultsWe developed the R package "tidyMicro" to serve as a more complete microbiome analysis pipeline. This open source software provides all of the essential tools available in other popular packages (e.g., management of sequence count tables, standard exploratory visualizations, and diversity inference tools) supplemented with multiple options for regression modelling (e.g., negative binomial, beta binomial, and/or rank based testing) and novel visualizations to improve interpretability (e.g., Rocky Mountain plots, longitudinal ordination plots). This comprehensive pipeline for microbiome analysis also maintains data structures familiar to R users to improve analysts' control over workflow. A complete vignette is provided to aid new users in analysis workflow.
conclusionstidyMicro provides a reliable alternative to popular microbiome analysis packages in R. We provide standard tools as well as novel extensions on standard analyses to improve interpretability results while maintaining object malleability to encourage open source collaboration. The simple examples and full workflow from the package are reproducible and applicable to external data sets.
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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.