IntegratedLearner/DESCRIPTION at master · himelmallick/IntegratedLearner · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
Package: IntegratedLearner
Type: Package
Title: Integrated Multi-Omics Learning for Survival and Other Outcomes
Version: 0.99.3
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 (>= 4.6.0)
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,
    multiview,
    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