DESCRIPTION

Package: SplineOmics
Type: Package
Title: Streamlines the process of analysing omics timeseries data with splines
Version: 0.1.0
Date: 2024-08-13
Authors@R: person("Thomas", "Rauter", 
                  email = "thomas.rauter@plus.ac.at", 
                  role = c("aut", "cre"),
                  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, with no missing values. Metadata about the samples 
 can be provided through a separate meta table, and an optional annotation 
 table can supply additional feature identifiers. The package provides several 
 capabilities: exploratory data analysis through HTML reports with plots like 
 PCA and heatmaps, hyperparameter screening for limma splines, and spline-based 
 limma analysis to identify significant features. Users can cluster these 
 significant features and perform gene set enrichment analysis (GSEA) on the 
 clusters. All results are presented in HTML reports to facilitate easy 
 interpretation and visualization.
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
Depends: R (>= 4.3.0)
Imports:
    ComplexHeatmap (>= 2.18.0),
    base64enc (>= 0.1-3),
    dendextend (>= 1.17.1),
    dplyr (>= 1.1.4),
    ggplot2 (>= 3.5.1),
    ggrepel (>= 0.9.5),
    here (>= 1.0.1),
    limma (>= 3.58.1),
    openxlsx (>= 4.2.5.2),
    patchwork (>= 1.2.0),
    pheatmap (>= 1.0.12),
    progress (>= 1.2.3),
    purrr (>= 1.0.2),
    rlang (>= 1.1.4),
    scales (>= 1.3.0),
    svglite (>= 2.1.3),
    tibble (>= 3.2.1),
    tidyr (>= 1.3.1),
    variancePartition (>= 1.14.0),
    zip (>= 2.3.1),
    grDevices,
    grid,
    splines,
    stats,
    tools,
    utils
Suggests:
    BiocManager,
    edgeR (>= 4.0.16),
    clusterProfiler (>= 4.10.1),
    rmarkdown (>= 2.7),
    knitr,
    testthat,
    readxl,
    rstudioapi (>= 0.16.0),
    conflicted (>= 1.2.0)
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.2
Config/testthat/edition: 3
VignetteBuilder: knitr