The DOI matches its Crossref record; 16 of the 16 references it cites were found in a registry or an index.
microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization
Open accessAbstract
Summary: Characterizing biomarkers based on microbiome profiles has great potential for translational medicine and precision medicine. Here, we present microbiomeMarker, an R/Bioconductor package implementing commonly used normalization and differential analysis (DA) methods, and three supervised learning models to identify microbiome markers. microbiomeMarker also allows comparison of different methods of DA and confounder analysis. It uses standardized input and output formats, which renders it highly scalable and extensible, and allows it to seamlessly interface with other microbiome packages and tools. In addition, the package provides a set of functions to visualize and interpret the identified microbiome markers. Availability and implementation: microbiomeMarker is freely available from Bioconductor (https://www.bioconductor.org/packages/microbiomeMarker). Source code is available and maintained at GitHub (https://github.com/yiluheihei/microbiomeMarker). Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
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QIIME allows analysis of high-throughput community sequencing data
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
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Self-citationphyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
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Cited by
Host Species and Environment Shape the Skin Microbiota of Mexican Axolotls
Soto-Cortés, E., Marroquín-Rodríguez, M., Basanta, M. D., Maldonado-López, Y., Parra-Olea, G., & Rebollar, E. A. (2024) · Microbial Ecology · doi:10.1007/s00248-024-02411-1 · Cited by 9
Metadata
- Authors
- Cao, Y., Dong, Q., Wang, D., Zhang, P., Liu, Y., & Niu, C.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-06-30
- Volume
- 38
- Issue
- 16
- Pages
- 4027-4029
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W4283721142
- Cited by
- 438
- References
- 16
- FWCI
- 24.51
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Cao, Y., Dong, Q., Wang, D., Zhang, P., Liu, Y., & Niu, C. (2022). microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac438
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