ArticleMicrobiome2021
animalcules: interactive microbiome analytics and visualization in R.
Article in Microbiome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 46 citations in OpenAlex.
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- Longitudinal Analysis of Nasopharyngeal Microbial Risk Markers for Fatal Acute Febrile Illness in a Zambian Birth Cohort.The Journal of infectious diseases · 2025Article
- Effects of zacopride and multidimensional impacts of cross-kingdom symbiosis: gut microbiota modulates coronary microvascular dysfunction via the chlorophyll/heme-tryptophan metabolic axis.Journal of translational medicine · 2025Article
- Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing.Microbiology (Reading, England) · 2025Article
- Reveal your microbes, and i'll reveal your origins: geographical traceability via Scomber colias intestinal tract metagenomics.Animal microbiome · 2025Article
- A comprehensive comparison of web-based tools for amplicon-metagenomic analysis.Frontiers in microbiology · 2025Review
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- iSEEtree: interactive explorer for hierarchical data.Bioinformatics advances · 2025Article
- Topical fluoride varnish application shifts dysbiotic dental plaque microbiome towards eubiosis in children with dental caries.The Saudi dental journal · 2024Article
- Marked genetic diversity withinInternational journal for parasitology. Parasites and wildlife · 2024Article
- Cereal leaf beetle-associated bacteria enhance the survival of their host upon insecticide treatments and respond differently to insecticides with different modes of action.Environmental microbiology reports · 2024Article
- Tools and methodology toFrontiers in microbiology · 2024Review
- The best practice for microbiome analysis using R.Protein & cell · 2023Article
- Analysis of nasopharyngeal microbiome patterns in Zambian infants with fatal acute febrile illness.bioRxiv : the preprint server for biology · 2023Article
- Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer.Human genomics · 2023Article
- Salivary microbiome and hypertension in the Qatari population.Journal of translational medicine · 2023Article
- The Effect of Dietary Supplementation with Zinc Amino Acids on Immunity, Antioxidant Capacity, and Gut Microbiota Composition in Calves.Animals : an open access journal from MDPI · 2023Article
- Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer.bioRxiv : the preprint server for biology · 2023Article
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Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
backgroundMicrobial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented resolution. However, these advances in data generation have presented novel challenges to researchers attempting to analyze and visualize these data.
resultsTo address some of these challenges, we have developed animalcules, an easy-to-use interactive microbiome analysis toolkit for 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-based metatranscriptomics profiling data. This toolkit combines novel and existing analytics, visualization methods, and machine learning models. For example, the toolkit features traditional microbiome analyses such as alpha/beta diversity and differential abundance analysis, combined with new methods for biomarker identification are. In addition, animalcules provides interactive and dynamic figures that enable users to understand their data and discover new insights. animalcules can be used as a standalone command-line R package or users can explore their data with the accompanying interactive R Shiny interface.
conclusionsWe present animalcules, an R package for interactive microbiome analysis through either an interactive interface facilitated by R Shiny or various command-line functions. It is the first microbiome analysis toolkit that supports the analysis of all 16S rRNA, DNA-based shotgun metagenomics, and RNA-sequencing based metatranscriptomics datasets. animalcules can be freely downloaded from GitHub at https://github.com/compbiomed/animalcules or installed through Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/animalcules.html . Video abstract.
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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.