Classification of low quality cells from single-cell RNA-seq data

Keywords

Biology, Embryonic stem cell, Computational biology, RNA, RNA-Seq

References

• Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastomaAnoop P. Patel, Itay Tirosh, John J. Trombetta — 2014
• RNA-Seq: a revolutionary tool for transcriptomicsZhong Wang, Mark Gerstein, M Snyder — 2009
• Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisionsCole Trapnell, Davide Cacchiarelli, Jonna Grimsby — 2014
• Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse BlastomeresFuchou Tang, Cátálin Bárbácioru, Ellen Nordman — 2011
• Single Cell Genomics: Advances and Future PerspectivesIain C. Macaulay, Thierry Voet — 2014
• Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune HomeostasisBidesh Mahata, Xiuwei Zhang, Aleksandra A. Kolodziejczyk — 2014
• Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cellsFlorian Buettner, Kedar Nath Natarajan, Francesco Paolo Casale — 2015
• Smart-seq2 for sensitive full-length transcriptome profiling in single cellsSimone Picelli, Åsa K. Björklund, Omid R. Faridani — 2013
• Count-based differential expression analysis of RNA sequencing data using R and BioconductorSimon Anders, Davis J. McCarthy, Yunshun Chen — 2013
• Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian CellsQiaolin Deng, Daniel Ramsköld, Björn Reinius — 2014
• Accounting for technical noise in single-cell RNA-seq experimentsPhilip Brennecke, Simon Anders, Jong Kim — 2013
• Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencingDmitry Usoskin, Alessandro Furlan, Saiful Islam — 2014
• Development and applications of single cell transcriptome analysisFuchou Tang, Kaiqin Lao, M. Azim Surani — 2011
• RNA sequencing: advances, challenges and opportunitiesFatih Ozsolak, Patrice M. Milos — 2010
• Reconstructing lineage hierarchies of the distal lung epithelium using single cell RNA-seqBarbara Treutlein, Douglas Brownfield, Angela Ruohao Wu — 2014
• Massively parallel single cell RNA-Seq for marker-free decomposition of tissues into cell typesDiego Adhemar Jaitin, Ephraim Kenigsberg, Hadas Keren‐Shaul — 2014
• Progressive increase in mtDNA 3243A>G heteroplasmy causes abrupt transcriptional reprogrammingMartin Picard, Jiangwen Zhang, Saege Hancock — 2014
• Quantitative single-cell RNA-seq with unique molecular identifiersSaiful Islam, Amit Zeisel, Simon Joost — 2013
• Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencingZhigang Xue, Kevin Huang, Chaochao Cai — 2013
• Multivariate outlier detection in exploration geochemistryPeter Filzmoser, R G Garrett, Clemens Reimann — 2005

Cited by

• Benchmarking full-length transcript single cell mRNA sequencing protocolsHarun Fitriyanto — 2020
• Design and computational analysis of single-cell RNA-sequencing experimentsRhonda Bacher, Christina Kendziorski — 2016
• Exploiting single-cell expression to characterize co-expression replicabilityMegan Crow, Anirban Paul, Sara Ballouz — 2016
• Single-Cell Transcriptome Analysis of Developing and Regenerating Spiral Ganglion NeuronsKelvin Y. Kwan — 2016
• Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas.Debarshi Mustafi, Brian M. Kevany, Xiaodong Bai — 2016
• A step-by-step workflow for low-level analysis of single-cell RNA-seq data with BioconductorAaron T. L. Lun, Davis J. McCarthy, John C. Marioni — 2016
• Single-Cell Transcriptomics Bioinformatics and Computational ChallengesOlivier Poirion, Xun Zhu, Travers Ching — 2016
• Single-Cell Isolation by Modular Single-Cell Pipette for RNA-SequencingKai Zhang, Min Gao, Zechen Chong — 2016
• Exploring viral infection using single-cell sequencing.Sylvie Rato, Monica Golumbeanu, Amalio Telenti — 2017
• Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetesNathan Lawlor, Joshy George, Mohan Bolisetty — 2017
• PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEXBrian D. Aevermann, Jamison McCorrison, Pratap Venepally — 2017
• Revealing the vectors of cellular identity with single-cell genomicsAllon Wagner, Aviv Regev, Nir Yosef — 2016
• Human dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c+ or CD141+ DCsGaëlle Breton, Shiwei Zheng, Renan Valieris — 2016
• How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.John C. Marioni, Detlev Arendt — 2017
• Single cell transcriptomics reveals unanticipated features of early hematopoietic precursorsJennifer Yang, Yoshiaki Tanaka, Montrell Seay — 2016
• Transcriptome-wide analysis in cells and tissuesS. Vickovic — 2017
• A cost effective 5΄ selective single cell transcriptome profiling approach with improved UMI designMarie‐Jeanne Arguel, Kévin Lebrigand, Agnès Paquet — 2016
• Seq-Well: A Portable, Low-Cost Platform for High-Throughput Single-Cell RNA-Seq of Low-Input SamplesTodd M. Gierahn, Marc H. Wadsworth, Travis K. Hughes — 2017
• Single-Cell Transcriptome Analysis of Neural Stem CellsYing Li, Jeremy Anderson, Kelvin Y. Kwan — 2017
• Cell fixation and preservation for droplet-based single-cell transcriptomicsJonathan Alles, Nikos Karaiskos, Samantha D. Praktiknjo — 2017

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