biblio.bib

@article{zeisel2018molecular,
  title={Molecular architecture of the mouse nervous system},
  author={Zeisel, Amit and Hochgerner, Hannah and L{\"o}nnerberg, Peter and Johnsson, Anna and Memic, Fatima and Van Der Zwan, Job and H{\"a}ring, Martin and Braun, Emelie and Borm, Lars E and La Manno, Gioele and others},
  journal={Cell},
  volume={174},
  number={4},
  pages={999--1014},
  year={2018},
  publisher={Elsevier}
}

@article{franzen2019panglaodb,
  title={PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data},
  author={Franz{\'e}n, Oscar and Gan, Li-Ming and Bj{\"o}rkegren, Johan LM},
  journal={Database},
  volume={2019},
  year={2019},
  publisher={Narnia}
}

@article{stuart2019comprehensive,
  title={Comprehensive integration of single-cell data},
  author={Stuart, Tim and Butler, Andrew and Hoffman, Paul and Hafemeister, Christoph and Papalexi, Efthymia and Mauck III, William M and Hao, Yuhan and Stoeckius, Marlon and Smibert, Peter and Satija, Rahul},
  journal={Cell},
  volume={177},
  number={7},
  pages={1888--1902},
  year={2019},
  publisher={Elsevier}
}

@article{luecken2019current,
  title={Current best practices in single-cell RNA-seq analysis: a tutorial},
  author={Luecken, Malte D and Theis, Fabian J},
  journal={Molecular systems biology},
  volume={15},
  number={6},
  pages={e8746},
  year={2019}
}

@misc{Romanhaa2020,
  author = {Hillje, R.},
  title = {scRNA-seq analysis workflow},
  year = {2020},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://romanhaa.github.io/projects/scrnaseq_workflow/}}
}

@Manual{scdbl,
  title = {scDblFinder: scDblFinder},
  author = {Pierre-Luc Germain},
  year = {2020},
  note = {R package version 1.2.0},
  url = {https://github.com/plger/scDblFinder},
}


@article{heimberg2016low,
  title={Low dimensionality in gene expression data enables the accurate extraction of transcriptional programs from shallow sequencing},
  author={Heimberg, Graham and Bhatnagar, Rajat and El-Samad, Hana and Thomson, Matt},
  journal={Cell systems},
  volume={2},
  number={4},
  pages={239--250},
  year={2016},
  publisher={Elsevier}
}


@article{maaten2008visualizing,
  title={Visualizing data using t-SNE},
  author={Maaten, Laurens van der and Hinton, Geoffrey},
  journal={Journal of machine learning research},
  volume={9},
  number={Nov},
  pages={2579--2605},
  year={2008}
}


@article{2018arXivUMAP,
     author = {{McInnes}, L. and {Healy}, J. and {Melville}, J.},
     title = "{UMAP: Uniform Manifold Approximation
     and Projection for Dimension Reduction}",
     journal = {ArXiv e-prints},
     archivePrefix = "arXiv",
     eprint = {1802.03426},
     primaryClass = "stat.ML",
     keywords = {Statistics - Machine Learning,
                 Computer Science - Computational Geometry,
                 Computer Science - Learning},
     year = 2018,
     month = feb,
}


@article{saunders2018molecular,
  title={Molecular diversity and specializations among the cells of the adult mouse brain},
  author={Saunders, Arpiar and Macosko, Evan Z and Wysoker, Alec and Goldman, Melissa and Krienen, Fenna M and de Rivera, Heather and Bien, Elizabeth and Baum, Matthew and Bortolin, Laura and Wang, Shuyu and others},
  journal={Cell},
  volume={174},
  number={4},
  pages={1015--1030},
  year={2018},
  publisher={Elsevier}
}

@article{zeisel2018molecular,
  title={Molecular architecture of the mouse nervous system},
  author={Zeisel, Amit and Hochgerner, Hannah and L{\"o}nnerberg, Peter and Johnsson, Anna and Memic, Fatima and Van Der Zwan, Job and H{\"a}ring, Martin and Braun, Emelie and Borm, Lars E and La Manno, Gioele and others},
  journal={Cell},
  volume={174},
  number={4},
  pages={999--1014},
  year={2018},
  publisher={Elsevier}
}