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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "Seqtometry" in publications use:'
type: software
license: MIT
title: 'Seqtometry: Signature scoring for single cell analysis'
version: 1.1.0
doi: 10.1016/j.cels.2023.12.005
identifiers:
- type: doi
  value: 10.32614/CRAN.package.Seqtometry
abstract: 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.
authors:
- family-names: Kousnetsov
  given-names: Robert
  email: robert.kousnetsov@health.slu.edu
preferred-citation:
  type: article
  title: Single-cell sequencing analysis within biologically relevant dimensions
  authors:
  - family-names: Kousnetsov
    given-names: Robert
    email: robert.kousnetsov@health.slu.edu
  - family-names: Bourque
    given-names: Jessica
  - family-names: Surnov
    given-names: Alexey
  - family-names: Fallahee
    given-names: Ian
  - family-names: Hawiger
    given-names: Daniel
  journal: Cell Systems
  year: '2024'
  volume: '15'
  issue: '1'
  doi: 10.1016/j.cels.2023.12.005
  start: 83-103.e11
repository: https://bioc.r-universe.dev
repository-code: https://github.com/HawigerLab/Seqtometry
commit: a787eb929f0d3ef2329f325eb97bc352363b114d
url: https://github.com/HawigerLab/Seqtometry
date-released: '2026-04-28'
contact:
- family-names: Kousnetsov
  given-names: Robert
  email: robert.kousnetsov@health.slu.edu