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@ARTICLE{Crowell2019-muscat,
  title    = "On the discovery of population-specific state transitions from
              multi-sample multi-condition single-cell {RNA} sequencing 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  = "bioRxiv",
  volume   =  713412,
  year     =  2019
}

@ARTICLE{Zhang2019,
  title   = "Probabilistic cell type assignment of single-cell transcriptomic
             data reveals spatiotemporal microenvironment dynamics in human
             cancers",
  author  = "Zhang, Allen W and O\textbackslashtextquoterightFlanagan, Ciara
             and Chavez, Elizabeth and Lim, Jamie L P and McPherson, Andrew and
             Wiens, Matt and Walters, Pascale and Chan, Tim and Hewitson,
             Brittany and Lai, Daniel and Mottok, Anja and Sarkozy, Clementine
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             Andrew P and McAlpine, Jessica N and Aparicio, Samuel and Steidl,
             Christian and Campbell, Kieran R and Shah, Sohrab P",
  journal = "bioRxiv",
  volume  =  521914,
  year    =  2019
}

@ARTICLE{Butler2018,
  title   = "Integrating single-cell transcriptomic data across different
             conditions, technologies, and species",
  author  = "Butler, Andrew and Hoffman, Paul and Smibert, Peter and Papalexi,
             Efthymia and Satija, Rahul",
  journal = "Nature Biotechnology",
  volume  =  36,
  number  =  5,
  pages   = "411--420",
  year    =  2018
}

@ARTICLE{Stuart2019,
  title   = "Comprehensive {I}ntegration of {{S}ingle-{C}ell} {D}ata",
  author  = "Stuart, Tim and Butler, Andrew and Hoffman, Paul and Hafemeister,
             Christoph and Papalexi, Efthymia and Mauck, 3rd, William M and
             Hao, Yuhan and Stoeckius, Marlon and Smibert, Peter and Satija,
             Rahul",
  journal = "Cell",
  volume  =  177,
  number  =  7,
  pages   = "1888--1902.e21",
  year    =  2019
}

@ARTICLE{Stegle2015,
  title   = "Computational and analytical challenges in single-cell
             transcriptomics",
  author  = "Stegle, Oliver and Teichmann, Sarah A and Marioni, John C",
  journal = "Nature Reviews Genetics",
  volume  =  16,
  number  =  3,
  pages   = "133--145",
  year    =  2015
}

@ARTICLE{Trapnell2015,
  title   = "Defining cell types and states with single-cell genomics",
  author  = "Trapnell, Cole",
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  volume  =  25,
  number  =  10,
  pages   = "1491--1498",
  year    =  2015
}

@ARTICLE{Wagner2016,
  title   = "Revealing the vectors of cellular identity with single-cell
             genomics",
  author  = "Wagner, Allon and Regev, Aviv and Yosef, Nir",
  journal = "Nature Biotechnology",
  volume  =  34,
  number  =  11,
  pages   = "1145--1160",
  year    =  2016
}

@ARTICLE{McCarthy2017-scater,
  title   = "Scater: pre-processing, quality control, normalization and
             visualization of single-cell {RNA-seq} data in {R}",
  author  = "McCarthy, Davis J and Campbell, Kieran R and Lun, Aaron T L and
             Wills, Quin F",
  journal = "Bioinformatics",
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  number  =  8,
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@ARTICLE{Love2014-DESeq2,
  title   = "Moderated estimation of fold change and dispersion for {RNA-seq}
             data with {DESeq2}",
  author  = "Love, Michael I and Huber, Wolfgang and Anders, Simon",
  journal = "Genome Biology",
  volume  =  15,
  number  =  12,
  pages   = "550",
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@ARTICLE{Korthauer2016-scDD,
  title   = "A statistical approach for identifying differential distributions
             in single-cell {RNA-seq} experiments",
  author  = "Korthauer, Keegan D and Chu, Li-Fang and Newton, Michael A and Li,
             Yuan and Thomson, James and Stewart, Ron and Kendziorski,
             Christina",
  journal = "Genome Biology",
  volume  =  17,
  number  =  1,
  pages   = "222",
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@ARTICLE{Kang2018-demuxlet,
  title   = "Multiplexed droplet single-cell {RNA-sequencing} using natural
             genetic variation",
  author  = "Kang, Hyun Min and Subramaniam, Meena and Targ, Sasha and Nguyen,
             Michelle and Maliskova, Lenka and McCarthy, Elizabeth and Wan,
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  journal = "Nature Biotechnology",
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@ARTICLE{Hafemeister2019-sctransform,
  title   = "Normalization and variance stabilization of single-cell {RNA-seq}
             data using regularized negative binomial regression",
  author  = "Hafemeister, Christoph and Satija, Rahul",
  journal = "bioRxiv",
  volume  =  576827,
  year    =  2019
}

@ARTICLE{Freytag2018,
  title    = "Comparison of clustering tools in {R} for medium-sized 10x
              Genomics single-cell {RNA-sequencing} data",
  author   = "Freytag, Saskia and Tian, Luyi and L{\"o}nnstedt, Ingrid and Ng,
              Milica and Bahlo, Melanie",
  journal  = "F1000Research",
  volume   =  7,
  pages    = "1297",
  year     =  2018
}

@ARTICLE{Duo2018,
  title   = "A systematic performance evaluation of clustering methods for
             single-cell {RNA-seq} data",
  author  = "Du{\`o}, Angelo and Robinson, Mark D and Soneson, Charlotte",
  journal = "F1000Research",
  volume  =  7,
  pages   = "1141",
  year    =  2018
}

@ARTICLE{Diaz-Mejia2019,
  title   = "Evaluation of methods to assign cell type labels to cell clusters
             from single-cell {RNA-sequencing} data",
  author  = "Diaz-Mejia, J Javier and Javier Diaz-Mejia, J and Meng, Elaine C
             and Pico, Alexander R and MacParland, Sonya A and Ketela, Troy and
             Pugh, Trevor J and Bader, Gary D and Morris, John H",
  journal = "F1000Research",
  volume  =  8,
  pages   = "296",
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}

@ARTICLE{Soneson2018,
  title   = "Bias, robustness and scalability in single-cell differential
             expression analysis",
  author  = "Soneson, Charlotte and Robinson, Mark D",
  journal = "Nature Methods",
  volume  =  15,
  number  =  4,
  pages   = "255--261",
  year    =  2018
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@ARTICLE{Ritchie2015-limma,
  title   = "limma powers differential expression analyses for {RNA-sequencing}
             and microarray studies",
  author  = "Ritchie, Matthew E and Phipson, Belinda and Wu, Di and Hu, Yifang
             and Law, Charity W and Shi, Wei and Smyth, Gordon K",
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  number  =  7,
  pages   = "e47",
  year    =  2015
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@ARTICLE{Robinson2010-edgeR,
  title   = "edge{R}: a {B}ioconductor package for differential expression
             analysis of digital gene expression data",
  author  = "Robinson, Mark D and McCarthy, Davis J and Smyth, Gordon K",
  journal = "Bioinformatics",
  volume  =  26,
  number  =  1,
  pages   = "139--140",
  year    =  2010
}
