LUCIDus: LUCID with Multiple Omics Data
Implements Latent Unknown Clusters By Integrating Multi-omics Data
(LUCID; Peng (2019) <doi:10.1093/bioinformatics/btz667>) for integrative
clustering with exposures, multi-omics data, and health outcomes.
Supports three integration strategies: early, parallel, and serial.
Provides model fitting and tuning, lasso-type regularization for exposure
and omics feature selection, handling of missing data, including both
sporadic and complete-case patterns, prediction, and g-computation for
estimating causal effects of exposures, bootstrap inference for
uncertainty estimation, and S3 summary and plot methods. For the
multi-omics integration framework, see Jia (2024)
<https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf>.
For the missing-data imputation mechanism, see Jia (2024)
<doi:10.1093/bioadv/vbae123>.
| Version: |
3.2.0 |
| Depends: |
R (≥ 3.6.0) |
| Imports: |
mclust, nnet, boot, jsonlite, networkD3, progress, stats, utils, glasso, glmnet, ggplot2, grDevices |
| Suggests: |
testthat (≥ 3.0.0), knitr, rmarkdown, plotly, mix, visdat |
| Published: |
2026-09-01 |
| DOI: |
10.32614/CRAN.package.LUCIDus |
| Author: |
Qiran Jia  [aut,
cre],
Yinqi Zhao [aut],
David Conti [ths],
Jesse Goodrich
[ctb] |
| Maintainer: |
Qiran Jia <qiranjia at usc.edu> |
| License: |
MIT + file LICENSE |
| URL: |
https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf,
https://doi.org/10.1093/bioadv/vbae123 |
| NeedsCompilation: |
no |
| Materials: |
NEWS |
| In views: |
MissingData, Omics |
| CRAN checks: |
LUCIDus results |
Documentation:
| Reference manual: |
LUCIDus.html , LUCIDus.pdf
|
| Vignettes: |
LUCID's Three Model Architectures: Early, Parallel, and Serial – Binary Outcome (HELIX Example) (source, R code)
LUCID's Three Model Architectures: Early, Parallel, and Serial – Continuous Outcome (HELIX Example) (source, R code)
LUCID Early Tutorial: Sankey Plot with Balanced Top Omics (source, R code)
LUCIDus Comprehensive Guide: Models, APIs, and End-to-End Functionality (source, R code)
LUCID Serial Tutorial: 6 Consecutive Parallel Stages with Monotone Missingness (source, R code)
|
Downloads:
Reverse dependencies:
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