DESCRIPTION

Package: SPATA2
Type: Package
Title: A Toolbox for Spatial Expression Analysis
Version: 3.1.3
Authors@R: as.person(c(
    "Jan Kueckelhaus <jan.kueckelhaus@uk-erlangen.de> [aut, cre]", 
    "Simon Frerich [ctb]",
    "Daniel Delev [ctb]",
    "Dieter-Henrik Heiland <dr.dieter.henrik.heiland@uniklinik-freiburg.de> [aut]" 
  ))
Description: This package provides a framework of functions and shiny-applications to make it as easy  and intuitive as possible to work with spatial expression data. 
Encoding: UTF-8
LazyData: true
License: GPL-3
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports: 
    aplot,
    broom,
    concaveman,
    colorspace,
    dbscan,
    dplyr,
    DT,
    FNN,
    ggalt,
    ggalluvial,
    ggforce,
    ggplot2,
    ggpubr,
    ggridges,
    ggsci,
    glue,
    grid,
    hdf5r,
    keys,
    lubridate,
    magick,
    magrittr,
    paletteer,
    pheatmap,
    pracma,
    progress,
    purrr,
    psych,
    rlang,
    readr,
    reticulate,
    scattermore,
    Seurat,
    shiny,
    shinyWidgets,
    shinybusy,
    shinydashboard,
    shinyhelper,
    sp,
    stringr,
    stringi,
    tibble,
    tidyr,
    tidytext,
    viridis,
    umap,
    units
Suggests:
    anndata
Collate: 
    'Geoms.R'
    'S4-documentation.R'
    'S4-generic-functions.R'
    'a.R'
    'add.R'
    'adj-aZ.R'
    'autoencoder.R'
    'b.R'
    'c.R'
    'check.R'
    'concept-documentation.R'
    'contains.R'
    'create.R'
    'createSpatialSegmentation.R'
    'd.R'
    'data.R'
    'deprecated_a-i.R'
    'deprecated_j-z.R'
    'dev.R'
    'discuss.R'
    'documentation-dummies.R'
    'downgrade.R'
    'e.R'
    'f.R'
    'g.R'
    'getA-G.R'
    'getH-M.R'
    'getN-Z.R'
    'h.R'
    'html.R'
    'i.R'
    'imported-functions.R'
    'initiateSpataObject.R'
    'j.R'
    'l.R'
    'm.R'
    'n.R'
    'new.R'
    'o.R'
    'p.R'
    'package-dependencies.R'
    'plotA-E.R'
    'plotF-G.R'
    'plotH-M.R'
    'plotN-S.R'
    'plotSurface.R'
    'plotT-Z.R'
    'plot_.R'
    'r-objects.R'
    'r.R'
    'runA-Z.R'
    's.R'
    'setA-Z.R'
    'shinyModules.R'
    't.R'
    'u.R'
    'unused.R'
    'v.R'
    'w.R'
Depends: 
    R (>= 3.5)
URL: https://themilolab.com/
References: 
    Kueckelhaus, J., Frerich, S., Kada-Benotmane, J., Koupourtidou, C., Ninkovic, J., 
    Dichgans, M., Beck, J., Schnell, O., & Heiland, D. H. (2024). 
    Inferring histology-associated gene expression gradients in spatial transcriptomic studies. 
    Nature Communications, 15, 7280. https://doi.org/10.1038/s41467-024-50904-x