SplineOmics/DESCRIPTION at main · csbg/SplineOmics · 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
78
79
80
81
82
83
84
85
86
87
88
89
90
91
Package: SplineOmics
Type: Package
Title: Streamlines the process of analysing omics timeseries data with splines
Version: 0.4.4
Authors@R:
    person("Thomas", "Rauter",
           email = "rauterthomas0@gmail.com",
           role = c("aut", "cre", "fnd"),
           comment = c(ORCID = "0009-0004-5578-3628"))
Description: SplineOmics streamlines the analysis of time-series omics data
 by fitting spline curves and using limma for hypothesis testing. It requires
 a data matrix with features (e.g., proteins, metabolites) in rows and time
 point samples in columns. Metadata about the samples can be provided through
 a separate meta table, and an optional annotation table can supply additional
 feature identifiers. Capabilities include exploratory data analysis (HTML
 reports with PCA, heatmaps, and related plots), spline-based limma analysis
 with optional automatic tuning of spline degrees of freedom via
 leave-one-out cross-validation, local peak-valley-cliff (PVC) excursion
 testing, clustering of significant features, over-representation analysis
 (ORA) with clusterProfiler enricher-style tests on clustered hits, comparison
 of two SplineOmics result objects, and gene-centric multi-omics clustering
 with UMAP visualization. Statistical computations are separated from HTML
 report generation where appropriate. Gene-set libraries can be obtained from
 Enrichr or Bioconductor organism databases.
License: MIT + file LICENSE
URL: https://csbg.github.io/SplineOmics
BugReports: https://github.com/csbg/SplineOmics/issues
biocViews: TimeCourse, GeneExpression, Proteomics, Metabolomics, Transcriptomics,
           Clustering, StatisticalMethod, Visualization, Software, GeneSetEnrichment,
           DifferentialExpression, BatchEffect
Depends: R (>= 4.5.0)
Imports:
    ComplexHeatmap (>= 2.18.0),
    ClusterR (>= 1.3.0),
    BiocParallel (>= 1.20.0),
    RhpcBLASctl (>= 0.21),
    variancePartition (>= 1.14.0),
    limma (>= 3.58.1),
    base64enc (>= 0.1-3),
    dplyr (>= 1.1.4),
    ggplot2 (>= 3.5.1),
    ggrepel (>= 0.9.5),
    writexl (>= 1.5.0),
    progress (>= 1.2.3),
    purrr (>= 1.0.2),
    pbapply (>= 1.5-0),
    rlang (>= 1.1.3),
    rstudioapi (>= 0.16.0),
    scales (>= 1.3.0),
    svglite (>= 2.1.3),
    tibble (>= 3.2.1),
    tidyr (>= 1.3.1),
    zip (>= 2.3.1),
    checkmate (>= 2.0.0),
    reformulas,
    grDevices,
    grid,
    splines,
    stats,
    tools,
    utils,
    car,
    methods
Suggests:
    AnnotationDbi,
    BiocManager,
    edgeR (>= 4.0.16),
    clusterProfiler (>= 4.10.1),
    curl (>= 7.0.0),
    gprofiler2 (>= 0.2.3),
    orthogene (>= 1.12.0),
    rmarkdown (>= 2.7),
    knitr,
    org.Mm.eg.db,
    testthat,
    readxl,
    conflicted (>= 1.2.0),
    readr,
    devtools,
    compositions,
    withr,
    ragg,
    uwot (>= 0.2.0),
    Matrix (>= 1.7),
    RSpectra (>= 0.16),
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0