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
NeedsCompilation: no
Packaged: 2025-12-04 10:00:20 UTC; diez
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>
Repository: CRAN
Date/Publication: 2025-12-04 14:40:02 UTC
Built: R 4.6.0; ; 2026-04-28 11:09:18 UTC; unix
