

@ARTICLE{Vieth2019-ld,
  title    = "A systematic evaluation of single cell {RNA-seq} analysis
              pipelines",
  author   = "Vieth, Beate and Parekh, Swati and Ziegenhain, Christoph and
              Enard, Wolfgang and Hellmann, Ines",
  journal  = "Nat. Commun.",
  volume   =  10,
  number   =  1,
  pages    = "4667",
  month    =  oct,
  year     =  2019,
  language = "en",
  issn     = "2041-1723",
  pmid     = "31604912",
  doi      = "10.1038/s41467-019-12266-7",
  pmc      = "PMC6789098"
}



@ARTICLE{Svensson2020-ip,
  title    = "Droplet {scRNA-seq} is not zero-inflated",
  author   = "Svensson, Valentine",
  journal  = "Nat. Biotechnol.",
  month    =  jan,
  year     =  2020,
  language = "en",
  issn     = "1087-0156, 1546-1696",
  pmid     = "31937974",
  doi      = "10.1038/s41587-019-0379-5"
}



@ARTICLE{Qiu2017-qa,
  title       = "Single-cell {mRNA} quantification and differential analysis
                 with Census",
  author      = "Qiu, Xiaojie and Hill, Andrew and Packer, Jonathan and Lin,
                 Dejun and Ma, Yi-An and Trapnell, Cole",
  affiliation = "Department of Genome Sciences, University of Washington,
                 Seattle, Washington, USA. Molecular and Cellular Biology
                 Program, University of Washington, Seattle, Washington, USA.
                 Department of Genome Sciences, University of Washington,
                 Seattle, Washington, USA. Department of Genome Sciences,
                 University of Washington, Seattle, Washington, USA. Department
                 of Genome Sciences, University of Washington, Seattle,
                 Washington, USA. Department of Applied Mathematics, University
                 of Washington, Seattle, Washington, USA. Department of Genome
                 Sciences, University of Washington, Seattle, Washington, USA.
                 Molecular and Cellular Biology Program, University of
                 Washington, Seattle, Washington, USA.",
  journal     = "Nat. Methods",
  month       =  "23~" # jan,
  year        =  2017,
  language    = "en",
  issn        = "1548-7091, 1548-7105",
  pmid        = "28114287",
  doi         = "10.1038/nmeth.4150"
}


@ARTICLE{Kim2015-zo,
  title    = "Characterizing noise structure in single-cell {RNA-seq}
              distinguishes genuine from technical stochastic allelic
              expression",
  author   = "Kim, Jong Kyoung and Kolodziejczyk, Aleksandra A and Illicic,
              Tomislav and Teichmann, Sarah A and Marioni, John C",
  journal  = "Nat. Commun.",
  volume   =  6,
  pages    = "8687",
  month    =  "22~" # oct,
  year     =  2015,
  keywords = "\#duplicates; bioinformatics; Biological sciences; Molecular
              biology",
  doi      = "10.1038/ncomms9687"
}


@ARTICLE{Vieth2017-lh,
  title    = "powsimR: power analysis for bulk and single cell {RNA-seq}
              experiments",
  author   = "Vieth, Beate and Ziegenhain, Christoph and Parekh, Swati and
              Enard, Wolfgang and Hellmann, Ines",
  journal  = "Bioinformatics",
  volume   =  33,
  number   =  21,
  pages    = "3486--3488",
  month    =  nov,
  year     =  2017,
  language = "en",
  issn     = "1367-4803, 1367-4811",
  pmid     = "29036287",
  doi      = "10.1093/bioinformatics/btx435"
}



@ARTICLE{Ziegenhain2017-sf,
  title    = "Comparative Analysis of {Single-Cell} {RNA} Sequencing Methods",
  author   = "Ziegenhain, Christoph and Vieth, Beate and Parekh, Swati and
              Reinius, Bj{\"o}rn and Guillaumet-Adkins, Amy and Smets, Martha
              and Leonhardt, Heinrich and Heyn, Holger and Hellmann, Ines and
              Enard, Wolfgang",
  journal  = "Mol. Cell",
  volume   =  65,
  number   =  4,
  pages    = "631--643.e4",
  month    =  "16~" # feb,
  year     =  2017,
  keywords = "single-cell RNA-seq; method comparison; transcriptomics; power
              analysis; simulation; cost-effectiveness",
  issn     = "1097-2765",
  doi      = "10.1016/j.molcel.2017.01.023"
}


@ARTICLE{Collado-Torres2017-mo,
  title       = "Reproducible {RNA-seq} analysis using recount2",
  author      = "Collado-Torres, Leonardo and Nellore, Abhinav and Kammers, Kai
                 and Ellis, Shannon E and Taub, Margaret A and Hansen, Kasper D
                 and Jaffe, Andrew E and Langmead, Ben and Leek, Jeffrey T",
  affiliation = "Department of Biostatistics, Johns Hopkins Bloomberg School of
                 Public Health, Baltimore, Maryland, USA. Center for
                 Computational Biology, Johns Hopkins University, Baltimore,
                 Maryland, USA. Lieber Institute for Brain Development, Johns
                 Hopkins Medical Campus, Baltimore, Maryland, USA. Department
                 of Biomedical Engineering, Oregon Health \&Science University,
                 Portland, Oregon, USA. Department of Surgery, Oregon Health
                 \&Science University, Portland, Oregon, USA. Computational
                 Biology Program, Oregon Health \&Science University, Portland,
                 Oregon, USA. Department of Biostatistics, Johns Hopkins
                 Bloomberg School of Public Health, Baltimore, Maryland, USA.
                 Center for Computational Biology, Johns Hopkins University,
                 Baltimore, Maryland, USA. Division of Biostatistics and
                 Bioinformatics, Department of Oncology, Sidney Kimmel
                 Comprehensive Cancer Center, Johns Hopkins University School
                 of Medicine, Baltimore, Maryland, USA. Department of
                 Biostatistics, Johns Hopkins Bloomberg School of Public
                 Health, Baltimore, Maryland, USA. Center for Computational
                 Biology, Johns Hopkins University, Baltimore, Maryland, USA.
                 Department of Biostatistics, Johns Hopkins Bloomberg School of
                 Public Health, Baltimore, Maryland, USA. Center for
                 Computational Biology, Johns Hopkins University, Baltimore,
                 Maryland, USA. Department of Biostatistics, Johns Hopkins
                 Bloomberg School of Public Health, Baltimore, Maryland, USA.
                 Center for Computational Biology, Johns Hopkins University,
                 Baltimore, Maryland, USA. McKusick-Nathans Institute of
                 Genetic Medicine, Johns Hopkins University, Baltimore,
                 Maryland, USA. Department of Biostatistics, Johns Hopkins
                 Bloomberg School of Public Health, Baltimore, Maryland, USA.
                 Center for Computational Biology, Johns Hopkins University,
                 Baltimore, Maryland, USA. Lieber Institute for Brain
                 Development, Johns Hopkins Medical Campus, Baltimore,
                 Maryland, USA. Department of Mental Health, Johns Hopkins
                 University, Baltimore, Maryland, USA. Department of
                 Biostatistics, Johns Hopkins Bloomberg School of Public
                 Health, Baltimore, Maryland, USA. Center for Computational
                 Biology, Johns Hopkins University, Baltimore, Maryland, USA.
                 Department of Computer Science, Johns Hopkins University,
                 Baltimore, Maryland, USA. Department of Biostatistics, Johns
                 Hopkins Bloomberg School of Public Health, Baltimore,
                 Maryland, USA. Center for Computational Biology, Johns Hopkins
                 University, Baltimore, Maryland, USA.",
  journal     = "Nat. Biotechnol.",
  volume      =  35,
  number      =  4,
  pages       = "319--321",
  month       =  "11~" # apr,
  year        =  2017,
  language    = "en",
  issn        = "1087-0156, 1546-1696",
  pmid        = "28398307",
  doi         = "10.1038/nbt.3838"
}

@ARTICLE{Wu2015-uj,
  title       = "{PROPER}: comprehensive power evaluation for differential
                 expression using {RNA-seq}",
  author      = "Wu, Hao and Wang, Chi and Wu, Zhijin",
  affiliation = "Department of Biostatistics and Bioinformatics, Emory
                 University, Atlanta, GA 30322, Department of Biostatistics and
                 Markey Cancer Center, University of Kentucky, Lexington, KY
                 40536 and Department of Biostatistics, Brown University,
                 Providence, RI 02806, USA. Department of Biostatistics and
                 Bioinformatics, Emory University, Atlanta, GA 30322,
                 Department of Biostatistics and Markey Cancer Center,
                 University of Kentucky, Lexington, KY 40536 and Department of
                 Biostatistics, Brown University, Providence, RI 02806, USA.
                 Department of Biostatistics and Bioinformatics, Emory
                 University, Atlanta, GA 30322, Department of Biostatistics and
                 Markey Cancer Center, University of Kentucky, Lexington, KY
                 40536 and Department of Biostatistics, Brown University,
                 Providence, RI 02806, USA.",
  journal     = "Bioinformatics",
  volume      =  31,
  number      =  2,
  pages       = "233--241",
  month       =  "15~" # jan,
  year        =  2015,
  language    = "en",
  issn        = "1367-4803, 1367-4811",
  pmid        = "25273110",
  doi         = "10.1093/bioinformatics/btu640",
  pmc         = "PMC4287952"
}


@ARTICLE{Mi2015-ri,
  title       = "Goodness-of-fit tests and model diagnostics for negative
                 binomial regression of {RNA} sequencing data",
  author      = "Mi, Gu and Di, Yanming and Schafer, Daniel W",
  affiliation = "Department of Statistics, Oregon State University, Corvallis,
                 Oregon, United States of America. Department of Statistics,
                 Oregon State University, Corvallis, Oregon, United States of
                 America; Molecular and Cellular Biology Program, Oregon State
                 University, Corvallis, Oregon, United States of America.
                 Department of Statistics, Oregon State University, Corvallis,
                 Oregon, United States of America.",
  journal     = "PLoS One",
  volume      =  10,
  number      =  3,
  pages       = "e0119254",
  month       =  "18~" # mar,
  year        =  2015,
  language    = "en",
  issn        = "1932-6203",
  pmid        = "25787144",
  doi         = "10.1371/journal.pone.0119254",
  pmc         = "PMC4365073"
}

@ARTICLE{Delignette-Muller2015-ie,
  title   = "fitdistrplus: An {R} Package for Fitting Distributions",
  author  = "Delignette-Muller, Marie and Dutang, Christophe",
  journal = "J. Stat. Softw.",
  volume  =  64,
  number  =  1,
  pages   = "1--34",
  year    =  2015,
  issn    = "1548-7660",
  doi     = "10.18637/jss.v064.i04"
}

@ARTICLE{Kolodziejczyk2015-vn,
  title       = "Single Cell {RNA-Sequencing} of Pluripotent States Unlocks
                 Modular Transcriptional Variation",
  author      = "Kolodziejczyk, Aleksandra A and Kim, Jong Kyoung and Tsang,
                 Jason C H and Ilicic, Tomislav and Henriksson, Johan and
                 Natarajan, Kedar N and Tuck, Alex C and Gao, Xuefei and
                 B{\"u}hler, Marc and Liu, Pentao and Marioni, John C and
                 Teichmann, Sarah A",
  affiliation = "European Molecular Biology Laboratory, European Bioinformatics
                 Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton,
                 Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute,
                 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
                 European Molecular Biology Laboratory, European Bioinformatics
                 Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton,
                 Cambridge CB10 1SD, UK. Wellcome Trust Sanger Institute,
                 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
                 European Molecular Biology Laboratory, European Bioinformatics
                 Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton,
                 Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute,
                 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
                 European Molecular Biology Laboratory, European Bioinformatics
                 Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton,
                 Cambridge CB10 1SD, UK. European Molecular Biology Laboratory,
                 European Bioinformatics Institute (EMBL-EBI), Wellcome Trust
                 Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust
                 Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
                 Cambridge CB10 1SA, UK. European Molecular Biology Laboratory,
                 European Bioinformatics Institute (EMBL-EBI), Wellcome Trust
                 Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Friedrich
                 Miescher Institute for Biomedical Research, Maulbeerstrasse
                 66, 4058 Basel, Switzerland. Wellcome Trust Sanger Institute,
                 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
                 Friedrich Miescher Institute for Biomedical Research,
                 Maulbeerstrasse 66, 4058 Basel, Switzerland. Wellcome Trust
                 Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
                 Cambridge CB10 1SA, UK. European Molecular Biology Laboratory,
                 European Bioinformatics Institute (EMBL-EBI), Wellcome Trust
                 Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust
                 Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
                 Cambridge CB10 1SA, UK; University of Cambridge, Cancer
                 Research UK Cambridge Institute, Robinson Way, Cambridge, CB2
                 0RE, UK. Electronic address: marioni@ebi.ac.uk. European
                 Molecular Biology Laboratory, European Bioinformatics
                 Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton,
                 Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute,
                 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
                 Electronic address: st9@sanger.ac.uk.",
  journal     = "Cell Stem Cell",
  volume      =  17,
  number      =  4,
  pages       = "471--485",
  month       =  "1~" # oct,
  year        =  2015,
  language    = "en",
  issn        = "1934-5909",
  pmid        = "26431182",
  doi         = "10.1016/j.stem.2015.09.011",
  pmc         = "PMC4595712"
}

@ARTICLE{Lun2016-ep,
  title       = "Pooling across cells to normalize single-cell {RNA} sequencing
                 data with many zero counts",
  author      = "Lun, Aaron T L and Bach, Karsten and Marioni, John C",
  affiliation = "Cancer Research UK Cambridge Institute, University of
                 Cambridge, Li Ka Shing Centre, Robinson Way, CB2 0RE,
                 Cambridge, UK. aaron.lun@cruk.cam.ac.uk. EMBL European
                 Bioinformatics Institute, Wellcome Genome Campus, Hinxton,
                 CB10 1SD, Cambridge, UK. Cancer Research UK Cambridge
                 Institute, University of Cambridge, Li Ka Shing Centre,
                 Robinson Way, CB2 0RE, Cambridge, UK. marioni@ebi.ac.uk. EMBL
                 European Bioinformatics Institute, Wellcome Genome Campus,
                 Hinxton, CB10 1SD, Cambridge, UK. marioni@ebi.ac.uk. Wellcome
                 Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10
                 1SA, Cambridge, UK. marioni@ebi.ac.uk.",
  journal     = "Genome Biol.",
  volume      =  17,
  pages       = "75",
  month       =  "27~" # apr,
  year        =  2016,
  keywords    = "Differential expression; Normalization; Single-cell RNA-seq",
  language    = "en",
  issn        = "1465-6906",
  pmid        = "27122128",
  doi         = "10.1186/s13059-016-0947-7",
  pmc         = "PMC4848819"
}

@ARTICLE{Love2014-je,
  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 Biol.",
  volume   =  15,
  number   =  12,
  pages    = "550",
  year     =  2014,
  language = "en",
  issn     = "1465-6906",
  pmid     = "25516281",
  doi      = "10.1186/s13059-014-0550-8",
  pmc      = "PMC4302049"
}

@ARTICLE{Robinson2010-ni,
  title       = "edgeR: a Bioconductor package for differential expression
                 analysis of digital gene expression data",
  author      = "Robinson, Mark D and McCarthy, Davis J and Smyth, Gordon K",
  affiliation = "Cancer Program, Garvan Institute of Medical Research, 384
                 Victoria Street, Darlinghurst, NSW 2010, Australia.
                 mrobinson@wehi.edu.au",
  journal     = "Bioinformatics",
  volume      =  26,
  number      =  1,
  pages       = "139--140",
  month       =  "1~" # jan,
  year        =  2010,
  language    = "en",
  issn        = "1367-4803, 1367-4811",
  pmid        = "19910308",
  doi         = "10.1093/bioinformatics/btp616",
  pmc         = "PMC2796818"
}

@ARTICLE{Delmans2016-ef,
  title       = "Discrete distributional differential expression ({D3E)--a}
                 tool for gene expression analysis of single-cell {RNA-seq}
                 data",
  author      = "Delmans, Mihails and Hemberg, Martin",
  affiliation = "Department of Plant Sciences, University of Cambridge, Downing
                 Street, Cambridge, CB2 3EA, UK. md656@cam.ac.uk. Wellcome
                 Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10
                 1SA, UK. mh26@sanger.ac.uk.",
  journal     = "BMC Bioinformatics",
  volume      =  17,
  pages       = "110",
  month       =  "29~" # feb,
  year        =  2016,
  language    = "en",
  issn        = "1471-2105",
  pmid        = "26927822",
  doi         = "10.1186/s12859-016-0944-6",
  pmc         = "PMC4772470"
}

@ARTICLE{Kim2013-qo,
  title    = "Inferring the kinetics of stochastic gene expression from
              single-cell {RNA-sequencing} data",
  author   = "Kim, Jong Kyoung and Marioni, John C",
  journal  = "Genome Biol.",
  volume   =  14,
  number   =  1,
  pages    = "R7",
  month    =  "28~" # jan,
  year     =  2013,
  language = "en",
  issn     = "1465-6906",
  pmid     = "23360624",
  doi      = "10.1186/gb-2013-14-1-r7",
  pmc      = "PMC3663116"
}

@BOOK{Colin_Cameron2013-vb,
  title     = "Regression Analysis of Count Data (Econometric Society
               Monographs)",
  author    = "Colin Cameron, A and Trivedi, Pravin K",
  publisher = "Cambridge University Press",
  edition   = "2 edition",
  month     =  "27~" # may,
  year      =  2013,
  language  = "en",
  isbn      = "9781107667273"
}


@ARTICLE{Soneson2018-xe,
  title    = "Bias, robustness and scalability in single-cell differential
              expression analysis",
  author   = "Soneson, Charlotte and Robinson, Mark D",
  journal  = "Nat. Methods",
  month    =  feb,
  year     =  2018,
  language = "en",
  issn     = "1548-7091, 1548-7105",
  pmid     = "29481549",
  doi      = "10.1038/nmeth.4612"
}


@article{Gentleman:2004,
  author =	 {Gentleman, Robert C and Carey, Vincent J and Bates,
                  Douglas M and Bolstad, Ben and Dettling, Marcel and
                  Dudoit, Sandrine and Ellis, Byron and Gautier,
                  Laurent and Ge, Yongchao and Gentry, Jeff and
                  Hornik, Kurt and Hothorn, Torsten and Huber,
                  Wolfgang and Iacus, Stefano and Irizarry, Rafael and
                  Leisch, Friedrich and Li, Cheng and Maechler, Martin
                  and Rossini, Anthony J and Sawitzki, Gunther and
                  Smith, Colin and Smyth, Gordon and Tierney, Luke and
                  Yang, Jean Y H and Zhang, Jianhua},
  title =	 {{Bioconductor: open software development for
                  computational biology and bioinformatics.}},
  journal =	 {Genome Biology},
  year =	 {2004},
  volume =	 {5},
  number =	 {10},
  pages =	 {R80},
  doi =		 {10.1186/gb-2004-5-10-r80},
  pubmed =	 {15461798}
}



@Article{10.1371/journal.pcbi.1003118,
  title = {Software for Computing and Annotating Genomic Ranges},
  Author = {Michael Lawrence and Wolfgang Huber and Herv\'e Pag\`es
                and Patrick Aboyoun and Marc Carlson and Robert
                Gentleman and Martin Morgan and Vincent Carey},
  year = 2013,
  journal = {{PLoS} Computational Biology},
  volume = 9,
  issue = 8,
  doi = {10.1371/journal.pcbi.1003118},
}

@Inbook{Leisch2002,
  author="Friedrich Leisch",
  editor="Wolfgang H{\"a}rdle and Bernd R{\"o}nz",
  chapter="Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis",
  title="Compstat: Proceedings in Computational Statistics",
  year="2002",
  publisher="Physica-Verlag HD",
  address="Heidelberg",
  pages="575--580",
  isbn="978-3-642-57489-4",
  doi="10.1007/978-3-642-57489-4_89",
  url="http://leisch.userweb.mwn.de/Sweave/"
}

@Book{Xie2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {http://yihui.name/knitr/},
}

@InCollection{Xie2014,
  booktitle = {Implementing Reproducible Computational Research},
  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2014},
  note = {ISBN 978-1466561595},
  url = {http://www.crcpress.com/product/isbn/9781466561595},
}


