Package: jazzPanda
Type: Package
Title: Finding spatially relevant marker genes in image based spatial
        transcriptomics data
Version: 1.3.0
Date: 2025-10-14
Authors@R: 
  c(person(given = "Melody",
           family = "Jin",
           role = c("aut", "cre"),
           email = "jin.m@wehi.edu.au",
           comment=c(ORCID="0000-0002-2222-0958"))
    )
LazyData: FALSE
Depends: R (>= 4.4.0)
Imports: spatstat.geom, dplyr, glmnet, caret, foreach, stats, magrittr,
        doParallel, BiocParallel, methods,
        BumpyMatrix,SpatialExperiment
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown, spatstat, Seurat, statmod,
        corrplot, ggplot2, ggraph, ggrepel, gridExtra, reshape2,
        igraph, jsonlite, vdiffr, patchwork, ggpubr, tidyr,
        SpatialFeatureExperiment, ExperimentHub, TENxXeniumData,
        SingleCellExperiment, SFEData, Matrix, data.table, scran,
        scater, grid, GenomeInfoDb, testthat (>= 3.0.0)
Description: This package contains the function to find marker genes
        for image-based spatial transcriptomics data. There are
        functions to create spatial vectors from the cell and
        transcript coordiantes, which are passed as inputs to find
        marker genes. Marker genes are detected for every cluster by
        two approaches. The first approach is by permtuation testing,
        which is implmented in parallel for finding marker genes for
        one sample study. The other approach is to build a linear model
        for every gene. This approach can account for multiple samples
        and backgound noise.
License: GPL-3
URL: https://github.com/phipsonlab/jazzPanda,
        https://bhuvad.github.io/jazzPanda/
BugReports: https://github.com/phipsonlab/jazzPanda/issues
biocViews: Spatial, GeneExpression, DifferentialExpression,
        StatisticalMethod, Transcriptomics
RoxygenNote: 7.3.2
Encoding: UTF-8
Config/testthat/edition: 3
Config/pak/sysreqs: libmagick++-dev gsfonts libicu-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:34:53 UTC
RemoteUrl: https://github.com/bioc/jazzPanda
RemoteRef: HEAD
RemoteSha: f913a8ba789eaad0a168caf569a2a4fb5056f761
NeedsCompilation: no
Packaged: 2026-01-09 21:31:02 UTC; root
Author: Melody Jin [aut, cre] (ORCID: <https://orcid.org/0000-0002-2222-0958>)
Maintainer: Melody Jin <jin.m@wehi.edu.au>
Built: R 4.6.0; ; 2026-01-09 21:34:48 UTC; windows
