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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 "scGate" in publications use:'
type: software
license: GPL-3.0-only
title: 'scGate: Marker-Based Cell Type Purification for Single-Cell Sequencing Data'
version: 1.6.2
identifiers:
- type: doi
  value: 10.32614/CRAN.package.scGate
abstract: 'A common bioinformatics task in single-cell data analysis is to purify
  a cell type or cell population of interest from heterogeneous datasets. ''scGate''
  automatizes marker-based purification of specific cell populations, without requiring
  training data or reference gene expression profiles. Briefly, ''scGate'' takes as
  input: i) a gene expression matrix stored in a ''Seurat'' object and ii) a “gating
  model” (GM), consisting of a set of marker genes that define the cell population
  of interest. The GM can be as simple as a single marker gene, or a combination of
  positive and negative markers. More complex GMs can be constructed in a hierarchical
  fashion, akin to gating strategies employed in flow cytometry. ''scGate'' evaluates
  the strength of signature marker expression in each cell using the rank-based method
  ''UCell'', and then performs k-nearest neighbor (kNN) smoothing by calculating the
  mean ''UCell'' score across neighboring cells. kNN-smoothing aims at compensating
  for the large degree of sparsity in scRNA-seq data. Finally, a universal threshold
  over kNN-smoothed signature scores is applied in binary decision trees generated
  from the user-provided gating model, to annotate cells as either “pure” or “impure”,
  with respect to the cell population of interest. See the related publication Andreatta
  et al. (2022) <https://doi.org/10.1093/bioinformatics/btac141>.'
authors:
- family-names: Andreatta
  given-names: Massimo
  email: massimo.andreatta@unil.ch
  orcid: https://orcid.org/0000-0002-8036-2647
- family-names: Berenstein
  given-names: Ariel
  email: arieljberenstein@gmail.com
  orcid: https://orcid.org/0000-0001-8540-5389
- family-names: Garnica
  given-names: Josep
  email: josep.garnicacaparros@unil.ch
- family-names: Carmona
  given-names: Santiago
  email: santiago.carmona@unil.ch
  orcid: https://orcid.org/0000-0002-2495-0671
preferred-citation:
  type: article
  title: 'scGate: marker-based purification of cell types from heterogeneous single-cell
    RNA-seq datasets'
  authors:
  - family-names: Andreatta
    given-names: Massimo
    email: massimo.andreatta@unil.ch
    orcid: https://orcid.org/0000-0002-8036-2647
  - family-names: Berenstein
    given-names: Ariel J.
  - family-names: Carmona
    given-names: Santiago J.
  journal: Bioinformatics
  year: '2022'
  volume: '38'
  start: 2642-2644
repository: https://carmonalab.r-universe.dev
repository-code: https://github.com/carmonalab/scGate
commit: 7d3189607d8a66d4e77c38932a0db0d9d8da7cb5
url: https://github.com/carmonalab/scGate
contact:
- family-names: Andreatta
  given-names: Massimo
  email: massimo.andreatta@unil.ch
  orcid: https://orcid.org/0000-0002-8036-2647