Package: IntegratedLearner
Type: Package
Title: Integrated Multi-Omics Learning for Survival and Other Outcomes
Version: 0.99.2
Authors@R: c(
    person("Nalin", "Arora", email = "naa4050@med.cornell.edu",
        role = c("aut", "cre", "cph"),
        comment = c(ORCID = "0009-0009-1340-688X")),
    person("Anupreet", "Porwal", role = "aut"),
    person("Himel", "Mallick", email = "him4004@med.cornell.edu",
        role = "aut",
        comment = c(ORCID = "0000-0003-4956-2429"))
    )
Description: Provides a unified interface for multi-omics prediction
        using early and late fusion for continuous, binary, multiclass,
        and survival outcomes. It supports both MultiAssayExperiment
        and PCL-style inputs, performs input validation and
        feature/sample harmonization across layers, and provides model
        fitting, prediction, plotting, and variable-importance
        utilities.
License: MIT + file LICENSE
URL: https://github.com/himelmallick/IntegratedLearner
BugReports: https://github.com/himelmallick/IntegratedLearner/issues
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: BART, CoxBoost, bayesplot, bayesreg, bartMachine, stats,
        utils, cowplot, ggplot2, gbm, glmnetUtils, mboost, nnet,
        nloptr, quadprog, randomForest, timeROC, SuperLearner,
        survival, glmnet, ranger, SummarizedExperiment,
        MultiAssayExperiment, caret, ROCR, dplyr, tibble, tidyr, withr,
        xgboost
Suggests: BiocStyle, mlbench, prediction, S4Vectors, testthat (>=
        3.0.0), knitr, rmarkdown
SystemRequirements: Java (optional; required for sl_bart / bartMachine
        workflows)
VignetteBuilder: knitr
biocViews: Software, Classification, Survival, Microbiome
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
RoxygenNote: 8.0.0
Config/pak/sysreqs: cmake make default-jdk libicu-dev libuv1-dev
        zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-08-03 19:49:23 UTC
RemoteUrl: https://github.com/BiocStaging/IntegratedLearner
RemoteRef: HEAD
RemoteSha: 6249b71983fcac8601e6bfaf4125fae85d7fe535
NeedsCompilation: no
Packaged: 2026-09-22 11:14:13 UTC; root
Author: Nalin Arora [aut, cre, cph] (ORCID:
    <https://orcid.org/0009-0009-1340-688X>),
  Anupreet Porwal [aut],
  Himel Mallick [aut] (ORCID: <https://orcid.org/0000-0003-4956-2429>)
Maintainer: Nalin Arora <naa4050@med.cornell.edu>