Package: CatsCradle
Title: This package provides methods for analysing spatial
        transcriptomics data and for discovering gene clusters
Version: 1.6.0
Authors@R: 
    c(person(given = "Anna",
        family = "Laddach",
        role = c("aut"),
        email = "anna.laddach@crick.ac.uk",
        comment = c(ORCID = "0000-0001-5552-6534")),
    person(given = "Michael",
        family = "Shapiro",
        role = c("aut","cre"),
        email = "michael.shapiro@crick.ac.uk",
        comment = c(ORCID = "0000-0002-2769-9320")))
Description: This package addresses two broad areas.  It allows for
        in-depth analysis of spatial transcriptomic data by identifying
        tissue neighbourhoods.  These are contiguous regions of tissue
        surrounding individual cells.  'CatsCradle' allows for the
        categorisation of neighbourhoods by the cell types contained in
        them and the genes expressed in them.  In particular, it
        produces Seurat objects whose individual elements are
        neighbourhoods rather than cells.  In addition, it enables the
        categorisation and annotation of genes by producing Seurat
        objects whose elements are genes.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: Seurat (>= 5.0.1), ggplot2, networkD3, stringr, pracma,
        reshape2, rdist, igraph, geometry, Rfast, data.table, abind,
        pheatmap, EBImage, S4Vectors, SeuratObject,
        SingleCellExperiment, SpatialExperiment, Matrix, methods,
        SummarizedExperiment, msigdbr
Suggests: fossil, interp, knitr, BiocStyle, tictoc
Depends: R (>= 4.4.0)
LazyData: false
VignetteBuilder: knitr
BugReports: https://github.com/AnnaLaddach/CatsCradle/issues
URL: https://github.com/AnnaLaddach/CatsCradle
biocViews: BiologicalQuestion, StatisticalMethod, GeneExpression,
        SingleCell, Transcriptomics, Spatial
NeedsCompilation: no
Packaged: 2026-04-29 18:44:05 UTC; root
Config/pak/sysreqs: cmake libfftw3-dev libglpk-dev make libmagick++-dev
        gsfonts libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:03:41 UTC
RemoteUrl: https://github.com/bioc/CatsCradle
RemoteRef: RELEASE_3_23
RemoteSha: bb3d7dade4e3802514c47cd793c5d75c9b143914
Author: Anna Laddach [aut] (ORCID: <https://orcid.org/0000-0001-5552-6534>),
  Michael Shapiro [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2769-9320>)
Maintainer: Michael Shapiro <michael.shapiro@crick.ac.uk>
Built: R 4.6.0; ; 2026-04-29 18:55:05 UTC; windows
