# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "singleCellTK" in publications use:'
type: software
license: MIT
title: 'singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq
  Data'
version: 2.15.0
abstract: The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface
  to popular tools for importing, quality control, analysis, and visualization of
  single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various
  packages at different stages of the analysis workflow. A general "a la carte" workflow
  gives users the ability access to multiple methods for data importing, calculation
  of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering,
  normalization, batch correction or integration, dimensionality reduction, 2-D embedding,
  clustering, marker detection, differential expression, cell type labeling, pathway
  analysis, and data exporting. Curated workflows can be used to run Seurat and Celda.
  Streamlined quality control can be performed on the command line using the SCTK-QC
  pipeline. Users can analyze their data using commands in the R console or by using
  an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire
  workflows can be summarized and shared with comprehensive HTML reports generated
  by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.
authors:
- family-names: Wang
  given-names: Yichen
  email: wangych@bu.edu
  orcid: https://orcid.org/0000-0003-4347-5199
- family-names: Sarfraz
  given-names: Irzam
  email: isarfraz@bu.edu
  orcid: https://orcid.org/0000-0001-8121-792X
- family-names: Hong
  given-names: Rui
  email: rzhong@bu.edu
- family-names: Koga
  given-names: Yusuke
  email: ykoga07@bu.edu
- family-names: Alabdullatif
  given-names: Salam
  email: salamha@bu.edu
- family-names: Pervaiz
  given-names: Nida
  email: nidapervaiz27@gmail.com
- family-names: Jenkins
  given-names: David
  email: dfj@bu.edu
  orcid: https://orcid.org/0000-0002-7451-4288
- family-names: Akavoor
  given-names: Vidya
  email: vidyaap@bu.edu
- family-names: Cao
  given-names: Xinyun
  email: xcao19@bu.edu
- family-names: Bandyadka
  given-names: Shruthi
  email: sbandya@bu.edu
- family-names: Leshchyk
  given-names: Anastasia
  email: aleshchk@bu.edu
- family-names: Faits
  given-names: Tyler
  email: tfaits@bu.edu
- family-names: Khan
  given-names: Mohammed Muzamil
  email: mmkhan@bu.edu
- family-names: Wang
  given-names: Zhe
  email: zhe@bu.edu
- family-names: Johnson
  given-names: W. Evan
  email: wej@bu.edu
  orcid: https://orcid.org/0000-0002-6247-6595
- family-names: Liu
  given-names: Ming
  email: mingl@bu.edu
- family-names: Campbell
  given-names: Joshua David
  email: camp@bu.edu
  orcid: https://orcid.org/0000-0003-0780-8662
repository: https://bioc.r-universe.dev
repository-code: https://github.com/compbiomed/singleCellTK
url: https://www.camplab.net/sctk/
contact:
- family-names: Campbell
  given-names: Joshua David
  email: camp@bu.edu
  orcid: https://orcid.org/0000-0003-0780-8662