Package: DamageDetective
Type: Package
Title: Detecting Damaged Cells in Single-Cell RNA Sequencing Data
Version: 2.0.15
Authors@R: 
    person("Alicen", "Henning", email = "alicen.jhb@gmail.com",
    role = c("aut", "cre", "cph"),
    comment = c(ORCID = "0009-0004-0535-1624"))
Description: Detects and filters damaged cells in single-cell RNA
        sequencing (scRNA-seq) data using a novel approach inspired by
        'DoubletFinder'. Damage is assessed by measuring how much each
        cell deviates from an artificially damaged version of itself,
        simulated through the probabilistic loss of cytoplasmic RNA.
        The method outputs a damage score ranging from 0 (viable,
        intact cell) to 1 (broken, non-viable cell), providing an
        intuitive scale for filtering that is standardised across cell
        types, sample origin, and experimental design.
License: AGPL (>= 3)
Encoding: UTF-8
Language: en-US
LazyData: false
RoxygenNote: 7.3.2
Depends: R (>= 3.5.0)
Roxygen: list(markdown = TRUE)
Imports: cowplot, dplyr, e1071, ggplot2, ggpubr, Matrix, patchwork,
        scales, Seurat, stringr, RcppHNSW, rlang, tidyr, withr, Rcpp
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://alicenjoyhenning.github.io/DamageDetective/,
        https://github.com/alicenjoyhenning/DamageDetective
BugReports: https://github.com/alicenjoyhenning/DamageDetective/issues
Config/testthat/edition: 3
LinkingTo: Rcpp, RcppArmadillo
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://alicenjoyhenning.r-universe.dev
Date/Publication: 2025-10-19 04:19:18 UTC
RemoteUrl: https://github.com/alicenjoyhenning/damagedetective
RemoteRef: HEAD
RemoteSha: 3d21be2175fcb29e9f68f301640e8386bf8a1c5c
NeedsCompilation: yes
Packaged: 2026-07-16 05:58:03 UTC; root
Author: Alicen Henning [aut, cre, cph] (ORCID:
    <https://orcid.org/0009-0004-0535-1624>)
Maintainer: Alicen Henning <alicen.jhb@gmail.com>