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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 "scPipe" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'scPipe: Pipeline for single cell multi-omic data pre-processing'
version: 2.5.0
abstract: A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts
  from the fastq files and produces a feature count matrix with associated quality
  control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq,
  Chromium 10x and SMART-seq protocols.
authors:
- family-names: Tian
  given-names: Luyi
  email: tian.l@wehi.edu.au
- family-names: Su
  given-names: Shian
  email: su.s@wehi.edu.au
- family-names: Amarasinghe
  given-names: Shani
  email: amarasinghe.s@wehi.edu.au
- family-names: Voogd
  given-names: Oliver
  email: voogd.o@wehi.edu.au
- family-names: Yang
  given-names: Phil
  email: yang.p@wehi.edu.au
preferred-citation:
  type: article
  title: 'scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell
    RNA-sequencing data'
  authors:
  - name: Tian
  - name: Luyi
  - name: Su
  - name: Shian
  - name: Dong
  - name: Xueyi
  - name: Amann-Zalcenstein
  - name: Daniela
  - name: Biben
  - name: Christine
  - name: Seidi
  - name: Azadeh
  - name: Hilton
  - family-names: J
    given-names: Douglas
  - name: Naik
  - family-names: H
    given-names: Shalin
  - name: Ritchie
  - family-names: E
    given-names: Matthew
  journal: PLoS computational biology
  volume: '14'
  issue: '8'
  year: '2018'
  publisher:
    name: Public Library of Science
  start: e1006361
repository: https://bioc.r-universe.dev
repository-code: https://github.com/LuyiTian/scPipe
url: https://github.com/LuyiTian/scPipe
date-released: '2022-10-12'
contact:
- family-names: Su
  given-names: Shian
  email: su.s@wehi.edu.au
references:
- type: article
  title: 'scPipe: An extended preprocessing pipeline for comprehensive single-cell
    ATAC-Seq data integration in R/Bioconductor'
  authors:
  - family-names: Amarasinghe
    given-names: Shanika L.
  - family-names: Yang
    given-names: Phil
  - family-names: Voogd
    given-names: Oliver
  - family-names: Yang
    given-names: Haoyu
  - family-names: Du
    given-names: Mei R. M.
  - family-names: Su
    given-names: Shian
  - family-names: Brown
    given-names: Daniel V.
  - family-names: Jabbari
    given-names: Jafar S.
  - family-names: Bowden
    given-names: Rory
  - family-names: Ritchie
    given-names: Matthew E.
  year: '2023'
  doi: 10.1101/2023.09.25.559230
  publisher:
    name: Cold Spring Harbor Laboratory
  url: https://www.biorxiv.org/content/early/2023/09/25/2023.09.25.559230
  journal: bioRxiv