Package: singleCellHaystack
Type: Package
Title: A Universal Differential Expression Prediction Tool for
        Single-Cell and Spatial Genomics Data
Version: 1.0.3
Authors@R: c(
    person("Alexis", "Vandenbon", email = "alexis.vandenbon@gmail.com", role = c("aut", "cre"),
        comment = c(ORCID = "0000-0003-2180-5732")),
    person("Diego", "Diez", email = "diego10ruiz@gmail.com", role = c("aut"),
        comment = c(ORCID = "0000-0002-2325-4893"))
    )
Description: One key exploratory analysis step in single-cell genomics
        data analysis is the prediction of features with different
        activity levels. For example, we want to predict differentially
        expressed genes (DEGs) in single-cell RNA-seq data, spatial
        DEGs in spatial transcriptomics data, or differentially
        accessible regions (DARs) in single-cell ATAC-seq data.
        'singleCellHaystack' predicts differentially active features in
        single cell omics datasets without relying on the clustering of
        cells into arbitrary clusters. 'singleCellHaystack' uses
        Kullback-Leibler divergence to find features (e.g., genes,
        genomic regions, etc) that are active in subsets of cells that
        are non-randomly positioned inside an input space (such as 1D
        trajectories, 2D tissue sections, multi-dimensional embeddings,
        etc). For the theoretical background of 'singleCellHaystack' we
        refer to our original paper Vandenbon and Diez (Nature
        Communications, 2020) <doi:10.1038/s41467-020-17900-3> and our
        update Vandenbon and Diez (Scientific Reports, 2023)
        <doi:10.1038/s41598-023-38965-2>.
Imports: methods, Matrix, splines, ggplot2, reshape2
Suggests: knitr, rmarkdown, testthat, SummarizedExperiment,
        SingleCellExperiment, SeuratObject, cowplot, wrswoR,
        sparseMatrixStats, ComplexHeatmap, patchwork
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://alexisvdb.github.io/singleCellHaystack/,
        https://github.com/alexisvdb/singleCellHaystack
BugReports: https://github.com/alexisvdb/singleCellHaystack/issues
LazyData: true
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Config/pak/sysreqs: libicu-dev
Repository: https://alexisvdb.r-universe.dev
Date/Publication: 2025-12-04 09:57:34 UTC
RemoteUrl: https://github.com/alexisvdb/singlecellhaystack
RemoteRef: HEAD
RemoteSha: 652e5d681dd23603b305c13884db050ba7f2a398
NeedsCompilation: no
Packaged: 2026-07-02 08:17:04 UTC; root
Author: Alexis Vandenbon [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2180-5732>),
  Diego Diez [aut] (ORCID: <https://orcid.org/0000-0002-2325-4893>)
Maintainer: Alexis Vandenbon <alexis.vandenbon@gmail.com>