DESCRIPTION

Package: scGate
Type: Package
Title: Marker-Based Cell Type Purification for Single-Cell Sequencing Data
Version: 1.6.2
Authors@R: c(
  person('Massimo', 'Andreatta',
    email = 'massimo.andreatta@unil.ch',
    role = c('aut','cre'),
    comment = c(ORCID = '0000-0002-8036-2647')), 
  person('Ariel','Berenstein',
    email = 'arieljberenstein@gmail.com',
    role = c('aut'),
    comment = c(ORCID = '0000-0001-8540-5389')), 
  person('Josep','Garnica',
    email = 'josep.garnicacaparros@unil.ch',
    role = c('aut')),  
  person('Santiago', 'Carmona',
    email = 'santiago.carmona@unil.ch',
    role = c('aut'),
    comment = c(ORCID = '0000-0002-2495-0671')) 
  )
Description: 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) <doi:10.1093/bioinformatics/btac141>.
biocViews:
Depends: R (>= 4.3.0)
Imports: Seurat (>= 4.0.0),
    UCell (>= 2.6.0),
    dplyr,
    stats,
    utils,
    methods,
    patchwork,
    ggridges,
    reshape2,
    ggplot2,
    BiocParallel
Suggests: ggparty,
    partykit,
    knitr,
    rmarkdown
VignetteBuilder: knitr
URL: https://github.com/carmonalab/scGate
BugReports: https://github.com/carmonalab/scGate/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3