Package: Seqtometry
Title: Signature scoring for single cell analysis
Version: 0.99.3
URL: https://github.com/HawigerLab/Seqtometry
BugReports: https://github.com/HawigerLab/Seqtometry/issues
Authors@R: c( 
    person("Robert", "Kousnetsov", email = "robert.kousnetsov@health.slu.edu", role = c("aut", "cre")),
    person("Daniel", "Hawiger", email = "daniel.hawiger@health.slu.edu", role = c("cph", "fnd")))
Description: This package provides functions used in Seqtometry
        (Kousnetsov et al. 2024), a method for analyzing single cell
        (scRNA-seq or scATAC-seq) data via signature (gene set)
        enrichment scores. The Seqtometry scores may be useful for
        annotating or characterizing cells, either in a flow cytometry
        like workflow (where scores are standalone features used for
        progressive partitoning as described in the Seqtometry
        publication) or in a cluster-based workflow (as features of
        clusters). The exported impute function (a port of Python's
        MAGIC-impute, van Dijk et al. 2018), may also be useful for
        single cell analysis on its own.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: R (>= 4.4.0)
LinkingTo: Rcpp, RcppArmadillo
Imports: BiocSingular, checkmate, data.table, future.apply, Matrix,
        MatrixGenerics, purrr, Rcpp, RcppHNSW, RSpectra, zeallot
Suggests: BiocStyle, box, dplyr, future, ggplot2, harmony, knitr, MASS,
        patchwork, rmarkdown, scater, scuttle, SingleCellExperiment,
        sparseMatrixStats, stringr, TENxPBMCData, testthat (>= 3.0.0),
        tibble
biocViews: SingleCell, GeneSetEnrichment, GeneExpression
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-03-26 00:47:58 UTC
RemoteUrl: https://github.com/bioc/Seqtometry
RemoteRef: HEAD
RemoteSha: b5415062087ec23ec807ff0ee9f8031330accc46
NeedsCompilation: yes
Packaged: 2026-03-26 13:44:50 UTC; root
Author: Robert Kousnetsov [aut, cre],
  Daniel Hawiger [cph, fnd]
Maintainer: Robert Kousnetsov <robert.kousnetsov@health.slu.edu>
Built: R 4.6.0; x86_64-w64-mingw32; 2026-03-26 13:47:43 UTC; windows
Archs: x64
