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@ARTICLE{Crowell2020-muscat,
  title   = "muscat detects subpopulation-specific state transitions from
             multi-sample multi-condition single-cell transcriptomics data",
  author  = "Crowell, Helena L and Soneson, Charlotte and Germain, Pierre-Luc
             and Calini, Daniela and Collin, Ludovic and Raposo, Catarina and
             Malhotra, Dheeraj and Robinson, Mark D",
  journal = "Nature Communications",
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  pages   = "6077",
  year    =  2020
}

@ARTICLE{Zhang2019,
  title   = "Probabilistic cell type assignment of single-cell transcriptomic
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  year    =  2019
}

@ARTICLE{Soneson2018-countsimQC,
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}

@ARTICLE{Butler2018-Seurat,
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@ARTICLE{Stuart2019,
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@ARTICLE{Stegle2015,
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@ARTICLE{Trapnell2015,
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@ARTICLE{Wagner2016,
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@ARTICLE{McCarthy2017-scater,
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@ARTICLE{Love2014-DESeq2,
  title   = "Moderated estimation of fold change and dispersion for {RNA-seq}
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@ARTICLE{Korthauer2016-scDD,
  title   = "A statistical approach for identifying differential distributions
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@ARTICLE{Kang2018-demuxlet,
  title   = "Multiplexed droplet single-cell {RNA-sequencing} using natural
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@ARTICLE{Soneson2016-iCOBRA,
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@ARTICLE{Hafemeister2019-sctransform,
  title   = "Normalization and variance stabilization of single-cell {RNA-seq}
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  volume  =  576827,
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@ARTICLE{Freytag2018-clustering,
  title    = "Comparison of clustering tools in {R} for medium-sized 10x
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@ARTICLE{Duo2018,
  title   = "A systematic performance evaluation of clustering methods for
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@ARTICLE{Diaz-Mejia2019,
  title   = "Evaluation of methods to assign cell type labels to cell clusters
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@ARTICLE{Soneson2018,
  title   = "Bias, robustness and scalability in single-cell differential
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@ARTICLE{Ritchie2015-limma,
  title   = "limma powers differential expression analyses for {RNA-sequencing}
             and microarray studies",
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@ARTICLE{Robinson2010-edgeR,
  title   = "edge{R}: a {B}ioconductor package for differential expression
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@ARTICLE{Gilis2023,
  title    = "Differential detection workflows for multi-sample single-cell
              {RNA-seq} data",
  author   = "Gilis, Jeroen and Perin, Laura and Malfait, Milan and Van den
              Berge, Koen and Takele Assefa, Alemu and Verbist, Bie and Risso,
              Davide and Clement, Lieven",
  journal  = "bioRxiv",
  year     =  2023
}

@ARTICLE{Bouland2021,
  title    = "Differential analysis of binarized single-cell {RNA} sequencing
              data captures biological variation",
  author   = "Bouland, Gerard A and Mahfouz, Ahmed and Reinders, Marcel J T",
  journal  = "NAR Genomics and Bioinformatics",
  volume   =  3,
  number   =  4,
  pages    = "lqab118",
  year     =  2021
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@ARTICLE{Qiu2020,
  title    = "Embracing the dropouts in single-cell {RNA-seq} analysis",
  author   = "Qiu, Peng",
  journal  = "Nature Communications",
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  number   =  1,
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@ARTICLE{Vandenberge2017,
  title    = "stageR: a general stage-wise method for controlling the gene-level
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  author   = "Van den Berge, Koen and Soneson, Charlotte and Robinson, Mark D 
	      and Clement, Lieven",
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@ARTICLE{Ignatiadis2016,
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@ARTICLE{Hu2010,
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}

