# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "muscat" in publications use:'
type: software
license: GPL-3.0-only
title: 'muscat: Multi-sample multi-group scRNA-seq data analysis tools'
version: 1.26.0
doi: 10.1038/s41467-020-19894-4
identifiers:
- type: doi
  value: 10.32614/CRAN.package.muscat
abstract: '`muscat` provides various methods and visualization tools for DS analysis
  in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including
  cell-level mixed models and methods based on aggregated “pseudobulk” data, as well
  as a flexible simulation platform that mimics both single and multi-sample scRNA-seq
  data.'
authors:
- family-names: Crowell
  given-names: Helena L.
  email: helena@crowell.eu
  orcid: https://orcid.org/0000-0002-4801-1767
- family-names: Germain
  given-names: Pierre-Luc
- family-names: Soneson
  given-names: Charlotte
- family-names: Sonrel
  given-names: Anthony
- family-names: Gilis
  given-names: Jeroen
- family-names: Risso
  given-names: Davide
- family-names: Clement
  given-names: Lieven
- family-names: Robinson
  given-names: Mark D.
  email: mark.robinson@imls.uzh.ch
preferred-citation:
  type: article
  title: muscat detects subpopulation-specific state transitions from multi-sample
    multi-condition single-cell transcriptomics data
  authors:
  - name: Crowell
  - family-names: L
    given-names: Helena
  - name: Soneson
  - name: Charlotte
  - name: Germain
  - name: Pierre-Luc
  - name: Calini
  - name: Daniela
  - name: Collin
  - name: Ludovic
  - name: Raposo
  - name: Catarina
  - name: Malhotra
  - name: Dheeraj
  - name: Robinson
  - family-names: D
    given-names: Mark
  journal: Nature Communications
  volume: '11'
  issue: '1'
  year: '2020'
  doi: 10.1038/s41467-020-19894-4
  start: '6077'
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/HelenaLC/muscat
commit: 861683175a1804430ced420397e72fff16fe92ed
url: https://github.com/HelenaLC/muscat
date-released: '2026-04-28'
contact:
- family-names: Crowell
  given-names: Helena L.
  email: helena@crowell.eu
  orcid: https://orcid.org/0000-0002-4801-1767
references:
- type: article
  title: Differential detection workflows for multi-sample single-cell RNA-seq data
  authors:
  - name: Gilis
  - name: Jeroen
  - name: Perin
  - name: Laura
  - name: Malfait
  - name: Milan
  - name: Crowell
  - family-names: L
    given-names: Helena
  - name: Van den Berge
  - name: Koen
  - name: Assefa
  - family-names: Takele
    given-names: Alemu
  - name: Verbist
  - name: Bie
  - name: Risso
  - name: Davide
  - name: Clement
  - name: Lieven
  journal: BMC Genomics
  volume: '26'
  issue: '1'
  year: '2025'
  doi: 10.1186/s12864-025-12102-x
  start: '886'
- type: article
  title: Bulk-based hypothesis weighing increases power in single-cell differential
    expression analysis
  authors:
  - name: Germain
  - name: Pierre-Luc
  - name: Wang
  - name: Jiayi
  - name: Robinson
  - family-names: D
    given-names: Mark
  journal: Peer Community Journal
  year: '2025'
  volume: '5'
  issue: e136
  doi: 10.24072/pcjournal.663