LUCIDus: LUCID with Multiple Omics Data

An implementation of estimating the Latent Unknown Clusters By Integrating Multi-omics Data (LUCID) model (Peng (2019) <doi:10.1093/bioinformatics/btz667>). LUCID conducts integrated clustering using exposures, omics information (and outcome information as an option). This package implements three different integration strategies for multi-omics data analysis within the LUCID framework: LUCID early integration (the original LUCID model), LUCID in parallel (intermediate integration), and LUCID in serial (late integration). Automated model selection for each LUCID model is available to obtain the optimal number of latent clusters, and an integrated imputation approach is implemented to handle sporadic and list-wise missingness in multi-omics data. Lasso-type regularity for exposure and omics features were added. S3 methods for summary and plotting functions were fixed. Fixed minor bugs.

Version:	3.0.3
Depends:	R (≥ 3.6.0)
Imports:	mclust, nnet, boot, jsonlite, networkD3, progress, stats, utils, glasso, glmnet
Suggests:	testthat (≥ 3.0.0)
Published:	2024-09-23
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
NeedsCompilation:	no
In views:	MissingData, Omics
CRAN checks:	LUCIDus results

Documentation:

Reference manual:

LUCIDus.pdf

Downloads:

Package source:	LUCIDus_3.0.3.tar.gz
Windows binaries:	r-devel: LUCIDus_3.0.3.zip, r-release: LUCIDus_3.0.3.zip, r-oldrel: LUCIDus_3.0.3.zip
macOS binaries:	r-release (arm64): LUCIDus_3.0.3.tgz, r-oldrel (arm64): LUCIDus_3.0.3.tgz, r-release (x86_64): LUCIDus_3.0.3.tgz, r-oldrel (x86_64): LUCIDus_3.0.3.tgz
Old sources:	LUCIDus archive

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