TY - JOUR AU - Macosko, E. Z. AU - Basu, A. AU - Satija, R. AU - Nemesh, J. AU - Shekhar, K. AU - Goldman, M. PY - 2015 DA - 2015// TI - Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets JO - Cell. VL - 161 UR - https://doi.org/10.1016/j.cell.2015.05.002 DO - 10.1016/j.cell.2015.05.002 ID - Macosko2015 ER - TY - JOUR AU - Zheng, G. X. Y. AU - Terry, J. M. AU - Belgrader, P. AU - Ryvkin, P. AU - Bent, Z. W. AU - Wilson, R. PY - 2017 DA - 2017// TI - Massively parallel digital transcriptional profiling of single cells JO - Nat Commun VL - 8 UR - https://doi.org/10.1038/ncomms14049 DO - 10.1038/ncomms14049 ID - Zheng2017 ER - TY - JOUR AU - Islam, S. AU - Zeisel, A. AU - Joost, S. AU - Manno, G. AU - Zajac, P. AU - Kasper, M. PY - 2014 DA - 2014// TI - Quantitative single-cell RNA-seq with unique molecular identifiers JO - Nat Methods VL - 11 UR - https://doi.org/10.1038/nmeth.2772 DO - 10.1038/nmeth.2772 ID - Islam2014 ER - TY - JOUR AU - Lun, A. T. L. AU - Riesenfeld, S. AU - Andrews, T. AU - Dao, T. P. AU - Gomes, T. AU - Marioni, J. C. PY - 2019 DA - 2019// TI - EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-019-1662-y DO - 10.1186/s13059-019-1662-y ID - Lun2019 ER - TY - JOUR AU - Mathys, H. AU - Davila-Velderrain, J. AU - Peng, Z. AU - Gao, F. AU - Mohammadi, S. AU - Young, J. Z. PY - 2019 DA - 2019// TI - Single-cell transcriptomic analysis of Alzheimer’s disease JO - Nature. VL - 570 UR - https://doi.org/10.1038/s41586-019-1195-2 DO - 10.1038/s41586-019-1195-2 ID - Mathys2019 ER - TY - JOUR AU - Dyer, C. A. AU - Kendler, A. AU - Jean-Guillaume, D. AU - Awatramani, R. AU - Lee, A. AU - Mason, L. M. PY - 2000 DA - 2000// TI - GFAP-positive and myelin marker-positive glia in normal and pathologic environments JO - J Neurosci Res VL - 60 UR - https://doi.org/3.0.CO;2-E DO - 3.0.CO;2-E ID - Dyer2000 ER - TY - JOUR AU - Wolock, S. L. AU - Lopez, R. AU - Klein, A. M. PY - 2019 DA - 2019// TI - Scrublet: computational identification of cell doublets in single-cell transcriptomic data JO - Cell Syst VL - 8 UR - https://doi.org/10.1016/j.cels.2018.11.005 DO - 10.1016/j.cels.2018.11.005 ID - Wolock2019 ER - TY - JOUR AU - DePasquale, E. A. K. AU - Schnell, D. J. AU - Camp, P. J. AU - Valiente-Alandí, Í. AU - Blaxall, B. C. AU - Grimes, H. L. PY - 2019 DA - 2019// TI - DoubletDecon: deconvoluting doublets from single-cell RNA-sequencing data JO - Cell Rep VL - 29 UR - https://doi.org/10.1016/j.celrep.2019.09.082 DO - 10.1016/j.celrep.2019.09.082 ID - DePasquale2019 ER - TY - JOUR AU - McGinnis, C. S. AU - Murrow, L. M. AU - Gartner, Z. J. PY - 2019 DA - 2019// TI - DoubletFinder: doublet detection in single-cell rna sequencing data using artificial nearest neighbors JO - Cell Syst VL - 8 UR - https://doi.org/10.1016/j.cels.2019.03.003 DO - 10.1016/j.cels.2019.03.003 ID - McGinnis2019 ER - TY - JOUR AU - Griffiths, J. A. AU - Richard, A. C. AU - Bach, K. AU - Lun, A. T. L. AU - Marioni, J. C. PY - 2018 DA - 2018// TI - Detection and removal of barcode swapping in single-cell RNA-seq data JO - Nat Commun VL - 9 UR - https://doi.org/10.1038/s41467-018-05083-x DO - 10.1038/s41467-018-05083-x ID - Griffiths2018 ER - TY - BOOK PY - 2019 DA - 2019// TI - R: A Language and Environment for Statistical Computing ID - ref11 ER - TY - JOUR AU - Lun, A. T. L. AU - McCarthy, D. J. AU - Marioni, J. C. PY - 2016 DA - 2016// TI - A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor JO - F1000Res VL - 5 ID - Lun2016 ER - TY - JOUR AU - Butler, A. AU - Hoffman, P. AU - Smibert, P. AU - Papalexi, E. AU - Satija, R. PY - 2018 DA - 2018// TI - Integrating single-cell transcriptomic data across different conditions, technologies, and species JO - Nat Biotechnol VL - 36 UR - https://doi.org/10.1038/nbt.4096 DO - 10.1038/nbt.4096 ID - Butler2018 ER - TY - JOUR AU - Stuart, T. AU - Butler, A. AU - Hoffman, P. AU - Hafemeister, C. AU - Papalexi, E. AU - Mauck, W. M. PY - 2019 DA - 2019// TI - Comprehensive integration of single-cell data JO - Cell VL - 177 UR - https://doi.org/10.1016/j.cell.2019.05.031 DO - 10.1016/j.cell.2019.05.031 ID - Stuart2019 ER - TY - BOOK AU - Wickham, H. PY - 2016 DA - 2016// TI - ggplot2: Elegant Graphics for Data Analysis UR - https://doi.org/10.1007/978-3-319-24277-4 DO - 10.1007/978-3-319-24277-4 ID - Wickham2016 ER - TY - JOUR AU - Gale, W. A. AU - Sampson, G. PY - 1995 DA - 1995// TI - Good-turing frequency estimation without tears* JO - J Quant Linguist VL - 2 UR - https://doi.org/10.1080/09296179508590051 DO - 10.1080/09296179508590051 ID - Gale1995 ER - TY - JOUR AU - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the false discovery rate: a practical and powerful approach to multiple testing JO - J R Stat Soc Ser B VL - 57 ID - Benjamini1995 ER - TY - JOUR AU - Mieth, B. AU - Kloft, M. AU - Rodríguez, J. A. AU - Sonnenburg, S. AU - Vobruba, R. AU - Morcillo-Suárez, C. PY - 2016 DA - 2016// TI - Combining multiple hypothesis testing with machine learning increases the statistical power of genome-wide association studies JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep36671 DO - 10.1038/srep36671 ID - Mieth2016 ER - TY - JOUR AU - Botía, J. A. AU - Vandrovcova, J. AU - Forabosco, P. AU - Guelfi, S. AU - D’Sa, K. AU - Hardy, J. PY - 2017 DA - 2017// TI - An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks JO - BMC Syst Biol VL - 11 UR - https://doi.org/10.1186/s12918-017-0420-6 DO - 10.1186/s12918-017-0420-6 ID - Botía2017 ER - TY - JOUR AU - Malik, L. AU - Almodaresi, F. AU - Patro, R. PY - 2018 DA - 2018// TI - Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis JO - Bioinformatics. VL - 34 UR - https://doi.org/10.1093/bioinformatics/bty378 DO - 10.1093/bioinformatics/bty378 ID - Malik2018 ER - TY - JOUR AU - Shannon, C. E. PY - 1948 DA - 1948// TI - A mathematical theory of communication JO - Bell Syst Tech J VL - 27 UR - https://doi.org/10.1002/j.1538-7305.1948.tb01338.x DO - 10.1002/j.1538-7305.1948.tb01338.x ID - Shannon1948 ER - TY - JOUR AU - Vento-Tormo, R. AU - Efremova, M. AU - Botting, R. A. AU - Turco, M. Y. AU - Vento-Tormo, M. AU - Meyer, K. B. PY - 2018 DA - 2018// TI - Single-cell reconstruction of the early maternal–fetal interface in humans JO - Nature. VL - 563 UR - https://doi.org/10.1038/s41586-018-0698-6 DO - 10.1038/s41586-018-0698-6 ID - Vento-Tormo2018 ER - TY - STD TI - Ni Z, Chen S, Brown J, Kendziorski C. CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data. GitHub. 2020. https://github.com/zijianni/scCB2. Accessed 15 May 2020. UR - https://github.com/zijianni/scCB2 ID - ref23 ER - TY - JOUR AU - Huber, W. AU - Carey, V. J. AU - Gentleman, R. AU - Anders, S. AU - Carlson, M. AU - Carvalho, B. S. PY - 2015 DA - 2015// TI - Orchestrating high-throughput genomic analysis with bioconductor JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3252 DO - 10.1038/nmeth.3252 ID - Huber2015 ER - TY - STD TI - Ni Z, Chen S, Brown J, Kendziorski C. CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data. Zenodo. 2020; https://doi.org/10.5281/zenodo.3829649. ID - ref25 ER -