TY - JOUR AU - Jiang, D. AU - Tang, C. AU - Zhang, A. PY - 2004 DA - 2004// TI - Cluster analysis for gene expression data: A survey JO - IEEE Trans Knowl Data Eng VL - 16 UR - https://doi.org/10.1109/TKDE.2004.68 DO - 10.1109/TKDE.2004.68 ID - Jiang2004 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. AU - Ziraldo, S. B. AU - Wheeler, T. D. AU - McDermott, G. P. AU - Zhu, J. AU - Gregory, M. T. AU - Shuga, J. AU - Montesclaros, L. AU - Underwood, J. G. AU - Masquelier, D. A. AU - Nishimura, S. Y. AU - Schnall-Levin, M. AU - Wyatt, P. W. AU - Hindson, C. M. AU - Bharadwaj, R. AU - Wong, A. AU - Ness, K. D. AU - Beppu, L. W. AU - Deeg, H. J. AU - McFarland, C. AU - Loeb, K. R. AU - Valente, W. J. AU - Ericson, N. G. AU - Stevens, E. A. AU - Radich, J. P. AU - Mikkelsen, T. S. AU - Hindson, B. J. AU - Bielas, J. H. 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 - Ilicic, T. AU - Kim, J. K. AU - Kolodziejczyk, A. A. AU - Bagger, F. O. AU - McCarthy, D. J. AU - Marioni, J. C. AU - Teichmann, S. A. PY - 2016 DA - 2016// TI - Classification of low quality cells from single-cell RNA-seq data JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-0888-1 DO - 10.1186/s13059-016-0888-1 ID - Ilicic2016 ER - TY - JOUR AU - Satija, R. AU - Farrell, J. A. AU - Gennert, D. AU - Schier, A. F. AU - Regev, A. PY - 2015 DA - 2015// TI - Spatial reconstruction of single-cell gene expression data JO - Nat Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3192 DO - 10.1038/nbt.3192 ID - Satija2015 ER - TY - JOUR AU - Segerstolpe, Å. AU - Palasantza, A. AU - Eliasson, P. AU - Andersson, E. -. M. AU - Andréasson, A. -. C. AU - Sun, X. AU - Picelli, S. AU - Sabirsh, A. AU - Clausen, M. AU - Bjursell, M. K. PY - 2016 DA - 2016// TI - Single-cell transcriptome profiling of human pancreatic islets in health and type 2 diabetes JO - Cell Metab VL - 24 UR - https://doi.org/10.1016/j.cmet.2016.08.020 DO - 10.1016/j.cmet.2016.08.020 ID - Segerstolpe2016 ER - TY - JOUR AU - Tibshirani, R. AU - Walther, G. AU - Hastie, T. PY - 2001 DA - 2001// TI - Estimating the number of clusters in a data set via the gap statistic JO - J R Stat Soc Ser B Stat Methodol VL - 63 UR - https://doi.org/10.1111/1467-9868.00293 DO - 10.1111/1467-9868.00293 ID - Tibshirani2001 ER - TY - JOUR AU - Zhu, X. AU - Wolfgruber, T. K. AU - Tasato, A. AU - Arisdakessian, C. AU - Garmire, D. G. AU - Garmire, L. X. PY - 2017 DA - 2017// TI - Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists JO - Genome Med VL - 9 UR - https://doi.org/10.1186/s13073-017-0492-3 DO - 10.1186/s13073-017-0492-3 ID - Zhu2017 ER - TY - JOUR AU - van der Maaten, L. J. P. AU - Hinton, G. E. PY - 2008 DA - 2008// TI - Visualizing high-dimensional data using t-sne JO - J Mach Learn Res VL - 9 ID - van der Maaten2008 ER - TY - STD TI - 10x Genomics. Cell Ranger R Kit Tutorial: Secondary Analysis on 10x Genomics Single Cell 30 RNA-seq PBMC Data. http://cf.10xgenomics.com/supp/cellexp/cellrangerrkit-PBMC-vignette-knitr-2.0.0.pdf. Accessed 16 July 2018. UR - http://cf.10xgenomics.com/supp/cellexp/cellrangerrkit-PBMC-vignette-knitr-2.0.0.pdf ID - ref9 ER - TY - JOUR AU - Blondel, V. D. AU - Guillaume, J. -. L. AU - Lambiotte, R. AU - Lefebvre, E. PY - 2008 DA - 2008// TI - Fast unfolding of communities in large networks JO - J Stat Mech Theory Exp VL - 2008 UR - https://doi.org/10.1088/1742-5468/2008/10/P10008 DO - 10.1088/1742-5468/2008/10/P10008 ID - Blondel2008 ER - TY - STD TI - Seurat - Guided Clustering Tutorial. https://satijalab.org/seurat/pbmc3k_tutorial.html. Accessed 16 July 2018. UR - https://satijalab.org/seurat/pbmc3k_tutorial.html ID - ref11 ER - TY - JOUR AU - Buettner, F. AU - Natarajan, K. N. AU - Casale, F. P. AU - Proserpio, V. AU - Scialdone, A. AU - Theis, F. J. AU - Teichmann, S. A. AU - Marioni, J. C. AU - Stegle, O. PY - 2015 DA - 2015// TI - Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells JO - Nat Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3102 DO - 10.1038/nbt.3102 ID - Buettner2015 ER - TY - STD TI - Fraley C, Raftery A, Murphy T, Scrucca L. mclust version 4 for r: Normal mixture modeling for model-based clustering, classification, and density estimation. 2012. ID - ref13 ER - TY - JOUR AU - Hartigan, J. A. AU - Wong, M. A. PY - 1979 DA - 1979// TI - Algorithm as 136: A k-means clustering algorithm JO - J R Stat Soc: Ser C: Appl Stat VL - 28 ID - Hartigan1979 ER - TY - JOUR AU - Hornik, K. AU - Feinerer, I. AU - Kober, M. AU - Buchta, C. PY - 2013 DA - 2013// TI - Spherical k-means clustering JO - J Stat Softw VL - 50 ID - Hornik2013 ER - TY - JOUR AU - Ward Jr, J. H. PY - 1963 DA - 1963// TI - Hierarchical grouping to optimize an objective function JO - J Am Stat Assoc VL - 58 UR - https://doi.org/10.1080/01621459.1963.10500845 DO - 10.1080/01621459.1963.10500845 ID - Ward Jr1963 ER - TY - JOUR AU - Csardi, G. AU - Nepusz, T. PY - 2006 DA - 2006// TI - The igraph software package for complex network research JO - InterJournal Complex Syst VL - 1695 ID - Csardi2006 ER - TY - BOOK AU - Leskovec, J. AU - Rajaraman, A. AU - Ullman, J. D. PY - 2014 DA - 2014// TI - Mining of Massive Datasets PB - Cambridge University Press CY - Cambridge UR - https://doi.org/10.1017/CBO9781139924801 DO - 10.1017/CBO9781139924801 ID - Leskovec2014 ER - TY - JOUR AU - Chen, H. -. I. H. AU - Jin, Y. AU - Huang, Y. AU - Chen, Y. PY - 2016 DA - 2016// TI - Detection of high variability in gene expression from single-cell RNA-seq profiling JO - BMC Genomics VL - 17 UR - https://doi.org/10.1186/s12864-016-2897-6 DO - 10.1186/s12864-016-2897-6 ID - Chen2016 ER - TY - STD TI - Dittenbach M. https://www.ir-facility.org/scoring-and-ranking-techniques-tf-idf-term-weighting-and-cosine-similarity. Accessed 16 July 2018. UR - https://www.ir-facility.org/scoring-and-ranking-techniques-tf-idf-term-weighting-and-cosine-similarity ID - ref20 ER - TY - JOUR AU - Clauset, A. AU - Newman, M. E. AU - Moore, C. PY - 2004 DA - 2004// TI - Finding community structure in very large networks JO - Phys Rev E VL - 70 UR - https://doi.org/10.1103/PhysRevE.70.066111 DO - 10.1103/PhysRevE.70.066111 ID - Clauset2004 ER - TY - JOUR AU - Lawlor, N. AU - George, J. AU - Bolisetty, M. AU - Kursawe, R. AU - Sun, L. AU - Sivakamasundari, V. AU - Kycia, I. AU - Robson, P. AU - Stitzel, M. L. PY - 2017 DA - 2017// TI - Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes JO - Genome Res VL - 27 UR - https://doi.org/10.1101/gr.212720.116 DO - 10.1101/gr.212720.116 ID - Lawlor2017 ER - TY - JOUR AU - Lee, C. AU - Mandoiu, I. I. AU - Nelson, C. E. PY - 2011 DA - 2011// TI - Inferring ethnicity from mitochondrial dna sequence JO - BMC Proceedings VL - 5 UR - https://doi.org/10.1186/1753-6561-5-S2-S11 DO - 10.1186/1753-6561-5-S2-S11 ID - Lee2011 ER - TY - STD TI - Van Asch V. Macro-and micro-averaged evaluation measures. Tech. Rep. 2013. ID - ref24 ER - TY - CHAP AU - Charikar, M. S. PY - 2002 DA - 2002// TI - Similarity estimation techniques from rounding algorithms BT - Proceedings of the Thiry-fourth Annual ACM Symposium on Theory of Computing PB - ACM CY - New York ID - Charikar2002 ER - TY - JOUR AU - Ondov, B. D. AU - Treangen, T. J. AU - Melsted, P. AU - Mallonee, A. B. AU - Bergman, N. H. AU - Koren, S. AU - Phillippy, A. M. PY - 2016 DA - 2016// TI - Mash: fast genome and metagenome distance estimation using minhash JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-0997-x DO - 10.1186/s13059-016-0997-x ID - Ondov2016 ER - TY - CHAP AU - Blekanov, V. AU - Korelin, V. PY - 2015 DA - 2015// TI - Hierarchical clustering of large text datasets using locality-sensitive hashing BT - Proceedings of the International Workshop on Applications in Information Technology PB - University of Aizu Press CY - Aizu-Wakamatsu ID - Blekanov2015 ER - TY - CHAP AU - Andoni, A. AU - Indyk, P. AU - Laarhoven, T. AU - Razenshteyn, I. AU - Schmidt, L. PY - 2015 DA - 2015// TI - Practical and optimal lsh for angular distance BT - Advances in Neural Information Processing Systems PB - Curran Associates CY - Red Hook ID - Andoni2015 ER - TY - CHAP AU - Eshghi, K. AU - Kafai, M. PY - 2016 DA - 2016// TI - The CRO kernel: Using concomitant rank order hashes for sparse high dimensional randomized feature maps BT - Data Engineering (ICDE), 32nd IEEE International Conference On PB - IEEE CY - Piscataway ID - Eshghi2016 ER - TY - CHAP AU - Ioffe, S. PY - 2010 DA - 2010// TI - Improved consistent sampling, weighted minhash and l1 sketching BT - Data Mining (ICDM), 2010 IEEE 10th International Conference On PB - IEEE CY - Piscataway ID - Ioffe2010 ER - TY - CHAP AU - Eshghi, K. AU - Rajaram, S. PY - 2008 DA - 2008// TI - Locality sensitive hash functions based on concomitant rank order statistics BT - Proceedings of the 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining PB - ACM CY - New York ID - Eshghi2008 ER - TY - STD TI - Wang J, Shen HT, Song J, Ji J. Hashing for similarity search: A survey. arXiv preprint arXiv:1408.2927. 2014. ID - ref32 ER - TY - STD TI - Cai Z, Daescu O, Li M. Proceedings of the 13th International Symposium on Bioinformatics Research and Applications, Honolulu, HI, USA, May 29–June 2, 2017, Lecture Notes in Computer Science vol. 10330: Springer; 2017. ID - ref33 ER -