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 (>= 4.5.0)
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
git_url: https://git.bioconductor.org/packages/Seqtometry
git_branch: devel
git_last_commit: b541506
git_last_commit_date: 2026-03-25
Repository: Bioconductor 3.24
Date/Publication: 2026-04-20
NeedsCompilation: yes
Packaged: 2026-04-21 00:47:17 UTC; biocbuild
Author: Robert Kousnetsov [aut, cre],
  Daniel Hawiger [cph, fnd]
Maintainer: Robert Kousnetsov <robert.kousnetsov@health.slu.edu>
