Convert files of some tools to microtable object of microeco package
Install file2meco package from CRAN.
if(!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
install.packages("file2meco", repos = BiocManager::repositories())
Chi Liu, Xiangzhen Li, Felipe R. P. Mansoldo, Tong Chen, Fanzheng Meng, Ruixiang Tang, Siyu Zhou, Qinghua Yang, Ruixin Shao & Minjie Yao. microeco 2: A comprehensive R package for downstream analysis of microbiome omics data. iMeta, 2026, 5: e70132. https://doi.org/10.1002/imt2.70132
Chi Liu, Felipe R. P. Mansoldo, Hankang Li, Alane Beatriz Vermelho, Raymond Jianxiong Zeng, Xiangzhen Li & Minjie Yao. A workflow for statistical analysis and visualization of microbiome omics data using the R microeco package. Nature Protocols, 2026, 21: 1300–1324. https://doi.org/10.1038/s41596-025-01239-4
https://chiliubio.github.io/microeco_tutorial/file2meco-package.html
Currently supported tools for data conversion include:
QIIME, QIIME2, HUMAnN, MetaPhlAn, Kraken2/Bracken, Ncyc, PICRUSt2, Tax4Fun/Tax4Fun2, ViromeScan, R package phyloseq and TreeSummarizedExperiment.
We welcome any contribution ! Any idea/suggestion will be considered. By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.