LOCOM2: A Logistic Regression Model for Testing Microbial Differential
Abundance
Testing differential abundance at individual taxa and in a whole microbial community. The tests are based on the log-ratio of relative abundances. The tests accommodate continuous, discrete (binary, categorical), and multivariate traits, and allow adjustment of confounders. For more details see He (2026) <doi:10.64898/2026.04.07.716976>. This package also includes the 'com2seq' function that combines two sequencing datasets (e.g., from 16S marker-gene and shotgun sequencing) for integrative analysis of differential abundance. For more details see <doi:10.1080/01621459.2025.2516205>.
| Version: |
1.1 |
| Depends: |
R (≥ 3.5.0) |
| Imports: |
Rcpp (≥ 1.0.11), stats, permute, parallel, BiocParallel, matrixStats, abind, car |
| LinkingTo: |
Rcpp, RcppArmadillo |
| Suggests: |
testthat, survival |
| Published: |
2026-10-29 |
| DOI: |
10.32614/CRAN.package.LOCOM2 |
| Author: |
Yi-Juan Hu [aut, cre] |
| Maintainer: |
Yi-Juan Hu <yijuanhu at bicmr.pku.edu.cn> |
| BugReports: |
https://github.com/yijuanhu/LOCOM2/issues |
| License: |
GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: |
https://github.com/yijuanhu/LOCOM2 |
| NeedsCompilation: |
yes |
| Materials: |
README |
| CRAN checks: |
LOCOM2 results |
Documentation:
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