Package: clustSIGNAL
Type: Package
Title: ClustSIGNAL: a spatial clustering method
Version: 1.2.0
Authors@R: c(
    person("Pratibha", "Panwar", email = "pratibhapanwar.4@gmail.com", 
    role = c("cre", "aut", "ctb"), comment = c(ORCID = "0000-0002-7437-7084")),
    person("Boyi", "Guo", email = "boyi.guo.work@gmail.com", role = "aut"),
    person("Haowen", "Zhao", email = "haowen.zhou19@gmail.com", role = "aut"),
    person("Stephanie", "Hicks", email = "shicks19@jhu.edu", role = "aut"),
    person("Shila", "Ghazanfar", email = "shazanfar@gmail.com", 
    role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-7861-6997")))
Description: clustSIGNAL: clustering of Spatially Informed Gene
        expression with Neighbourhood Adapted Learning. A tool for
        adaptively smoothing and clustering gene expression data.
        clustSIGNAL uses entropy to measure heterogeneity of cell
        neighbourhoods and performs a weighted, adaptive smoothing,
        where homogeneous neighbourhoods are smoothed more and
        heterogeneous neighbourhoods are smoothed less. This not only
        overcomes data sparsity but also incorporates spatial context
        into the gene expression data. The resulting smoothed gene
        expression data is used for clustering and could be used for
        other downstream analyses.
License: GPL-2
Encoding: UTF-8
URL: https://sydneybiox.github.io/clustSIGNAL/
BugReports: https://github.com/sydneybiox/clustSIGNAL/issues
biocViews: Clustering, Software, GeneExpression, Spatial,
        Transcriptomics, SingleCell
RoxygenNote: 7.3.2
Depends: R (>= 4.4.0), SpatialExperiment
Imports: BiocParallel, BiocNeighbors, bluster (>= 1.16.0), scater,
        harmony, SingleCellExperiment, SummarizedExperiment, methods,
        Matrix, reshape2
Suggests: knitr, BiocStyle, testthat (>= 3.0.0), aricode, ggplot2,
        patchwork, dplyr, scattermore
VignetteBuilder: knitr
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        libfribidi-dev libglpk-dev libharfbuzz-dev libmagick++-dev
        gsfonts libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libwebp-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:35:51 UTC
RemoteUrl: https://github.com/bioc/clustSIGNAL
RemoteRef: RELEASE_3_22
RemoteSha: 55aa2e19e9e66de7d1bd36a6adf6da3921ba5a16
NeedsCompilation: no
Packaged: 2026-02-03 08:44:24 UTC; root
Author: Pratibha Panwar [cre, aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-7437-7084>),
  Boyi Guo [aut],
  Haowen Zhao [aut],
  Stephanie Hicks [aut],
  Shila Ghazanfar [aut, ctb] (ORCID:
    <https://orcid.org/0000-0001-7861-6997>)
Maintainer: Pratibha Panwar <pratibhapanwar.4@gmail.com>
Built: R 4.5.2; ; 2026-02-03 08:46:55 UTC; windows
