TY - JOUR AU - Wang, Z. AU - Gerstein, M. AU - Snyder, M. PY - 2009 DA - 2009// TI - RNA-Seq: a revolutionary tool for transcriptomics JO - Nat Rev Genet VL - 10 UR - https://doi.org/10.1038/nrg2484 DO - 10.1038/nrg2484 ID - Wang2009 ER - TY - JOUR AU - Marguerat, S. AU - Bahler, J. PY - 2010 DA - 2010// TI - RNA-seq: from technology to biology JO - Cell Mol Life Sci VL - 67 UR - https://doi.org/10.1007/s00018-009-0180-6 DO - 10.1007/s00018-009-0180-6 ID - Marguerat2010 ER - TY - JOUR AU - Robertson, G. AU - Schein, J. AU - Chiu, R. AU - Corbett, R. AU - Field, M. AU - Jackman, S. D. PY - 2010 DA - 2010// TI - De novo assembly and analysis of RNA-seq data JO - Nat Methods VL - 7 UR - https://doi.org/10.1038/nmeth.1517 DO - 10.1038/nmeth.1517 ID - Robertson2010 ER - TY - JOUR AU - Schliebner, I. AU - Becher, R. AU - Hempel, M. AU - Deising, H. B. AU - Horbach, R. PY - 2014 DA - 2014// TI - New gene models and alternative splicing in the maize pathogen Colletotrichum graminicola revealed by RNA-Seq analysis JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-842 DO - 10.1186/1471-2164-15-842 ID - Schliebner2014 ER - TY - JOUR AU - Canovas, A. AU - Rincon, G. AU - Islas-Trejo, A. AU - Wickramasinghe, S. AU - Medrano, J. F. PY - 2010 DA - 2010// TI - SNP discovery in the bovine milk transcriptome using RNA-Seq technology JO - Mamm Genome VL - 21 UR - https://doi.org/10.1007/s00335-010-9297-z DO - 10.1007/s00335-010-9297-z ID - Canovas2010 ER - TY - JOUR AU - Piskol, R. AU - Ramaswami, G. AU - Li, J. B. PY - 2013 DA - 2013// TI - Reliable identification of genomic variants from RNA-seq data JO - Am J Hum Genet VL - 93 UR - https://doi.org/10.1016/j.ajhg.2013.08.008 DO - 10.1016/j.ajhg.2013.08.008 ID - Piskol2013 ER - TY - JOUR AU - Wang, L. AU - Feng, Z. AU - Wang, X. AU - Wang, X. AU - Zhang, X. PY - 2010 DA - 2010// TI - DEGseq: an R package for identifying differentially expressed genes from RNA-seq data JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp612 DO - 10.1093/bioinformatics/btp612 ID - Wang2010 ER - TY - JOUR AU - Ellard, S. AU - Patrinos, G. P. AU - Oetting, W. S. PY - 2013 DA - 2013// TI - Clinical applications of next-generation sequencing: the 2013 human genome variation society scientific meeting JO - Hum Mutat VL - 34 UR - https://doi.org/10.1002/humu.22400 DO - 10.1002/humu.22400 ID - Ellard2013 ER - TY - JOUR AU - Byron, S. A. AU - Keuren-Jensen, K. R. AU - Engelthaler, D. M. AU - Carpten, J. D. AU - Craig, D. W. PY - 2016 DA - 2016// TI - Translating RNA sequencing into clinical diagnostics: opportunities and challenges JO - Nat Rev Genet VL - 17 UR - https://doi.org/10.1038/nrg.2016.10 DO - 10.1038/nrg.2016.10 ID - Byron2016 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Dobin, A. AU - Davis, C. A. AU - Schlesinger, F. AU - Drenkow, J. AU - Zaleski, C. AU - Jha, S. PY - 2013 DA - 2013// TI - STAR: ultrafast universal RNA-seq aligner JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts635 DO - 10.1093/bioinformatics/bts635 ID - Dobin2013 ER - TY - JOUR AU - Trapnell, C. AU - Pachter, L. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - TopHat: discovering splice junctions with RNA-Seq JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp120 DO - 10.1093/bioinformatics/btp120 ID - Trapnell2009 ER - TY - JOUR AU - Kim, D. AU - Langmead, B. AU - Salzberg, S. L. PY - 2015 DA - 2015// TI - HISAT: a fast spliced aligner with low memory requirements JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3317 DO - 10.1038/nmeth.3317 ID - Kim2015 ER - TY - JOUR AU - Kim, D. AU - Pertea, G. AU - Trapnell, C. AU - Pimentel, H. AU - Kelley, R. AU - Salzberg, S. L. PY - 2013 DA - 2013// TI - TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-4-r36 DO - 10.1186/gb-2013-14-4-r36 ID - Kim2013 ER - TY - JOUR AU - Zeng, W. AU - Mortazavi, A. PY - 2012 DA - 2012// TI - Technical considerations for functional sequencing assays JO - Nat Immunol VL - 13 UR - https://doi.org/10.1038/ni.2407 DO - 10.1038/ni.2407 ID - Zeng2012 ER - TY - JOUR AU - Robinson, M. D. AU - Oshlack, A. PY - 2010 DA - 2010// TI - A scaling normalization method for differential expression analysis of RNA-seq data JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-3-r25 DO - 10.1186/gb-2010-11-3-r25 ID - Robinson2010 ER - TY - JOUR AU - Bullard, J. H. AU - Purdom, E. AU - Hansen, K. D. AU - Dudoit, S. PY - 2010 DA - 2010// TI - Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-94 DO - 10.1186/1471-2105-11-94 ID - Bullard2010 ER - TY - JOUR AU - Li, X. AU - Brock, G. N. AU - Rouchka, E. C. AU - Cooper, N. G. F. AU - Wu, D. AU - O'Toole, T. E. PY - 2017 DA - 2017// TI - A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data JO - PLoS One VL - 12 UR - https://doi.org/10.1371/journal.pone.0176185 DO - 10.1371/journal.pone.0176185 ID - Li2017 ER - TY - JOUR AU - Mortazavi, A. AU - Williams, B. A. AU - McCue, K. AU - Schaeffer, L. AU - Wold, B. PY - 2008 DA - 2008// TI - Mapping and quantifying mammalian transcriptomes by RNA-Seq JO - Nat Methods VL - 5 UR - https://doi.org/10.1038/nmeth.1226 DO - 10.1038/nmeth.1226 ID - Mortazavi2008 ER - TY - JOUR AU - Marioni, J. C. AU - Mason, C. E. AU - Mane, S. M. AU - Stephens, M. AU - Gilad, Y. PY - 2008 DA - 2008// TI - RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.079558.108 DO - 10.1101/gr.079558.108 ID - Marioni2008 ER - TY - JOUR AU - Trapnell, C. AU - Williams, B. A. AU - Pertea, G. AU - Mortazavi, A. AU - Kwan, G. AU - Baren, M. J. PY - 2010 DA - 2010// TI - Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1621 DO - 10.1038/nbt.1621 ID - Trapnell2010 ER - TY - JOUR AU - Trapnell, C. AU - Roberts, A. AU - Goff, L. AU - Pertea, G. AU - Kim, D. AU - Kelley, D. R. PY - 2012 DA - 2012// TI - Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks JO - Nat Protoc VL - 7 UR - https://doi.org/10.1038/nprot.2012.016 DO - 10.1038/nprot.2012.016 ID - Trapnell2012 ER - TY - JOUR AU - Dillies, M. A. AU - Rau, A. AU - Aubert, J. AU - Hennequet-Antier, C. AU - Jeanmougin, M. AU - Servant, N. PY - 2013 DA - 2013// TI - A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis JO - Brief Bioinform VL - 14 UR - https://doi.org/10.1093/bib/bbs046 DO - 10.1093/bib/bbs046 ID - Dillies2013 ER - TY - JOUR AU - Smyth, G. K. PY - 2004 DA - 2004// TI - Linear models and empirical bayes methods for assessing differential expression in microarray experiments JO - Stat Appl Genet Mol Biol VL - 3 UR - https://doi.org/10.2202/1544-6115.1027 DO - 10.2202/1544-6115.1027 ID - Smyth2004 ER - TY - JOUR AU - Love, M. I. AU - Huber, W. AU - Anders, S. PY - 2014 DA - 2014// TI - Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0550-8 DO - 10.1186/s13059-014-0550-8 ID - Love2014 ER - TY - JOUR AU - Anders, S. AU - Huber, W. PY - 2010 DA - 2010// TI - Differential expression analysis for sequence count data JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-10-r106 DO - 10.1186/gb-2010-11-10-r106 ID - Anders2010 ER - TY - JOUR AU - Risso, D. AU - Ngai, J. AU - Speed, T. P. AU - Dudoit, S. PY - 2014 DA - 2014// TI - Normalization of RNA-seq data using factor analysis of control genes or samples JO - Nat Biotechnol VL - 32 UR - https://doi.org/10.1038/nbt.2931 DO - 10.1038/nbt.2931 ID - Risso2014 ER - TY - JOUR AU - Risso, D. AU - Schwartz, K. AU - Sherlock, G. AU - Dudoit, S. PY - 2011 DA - 2011// TI - GC-content normalization for RNA-Seq data JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-480 DO - 10.1186/1471-2105-12-480 ID - Risso2011 ER - TY - JOUR AU - Law, C. W. AU - Chen, Y. AU - Shi, W. AU - Smyth, G. K. PY - 2014 DA - 2014// TI - voom: precision weights unlock linear model analysis tools for RNA-seq read counts JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/gb-2014-15-2-r29 DO - 10.1186/gb-2014-15-2-r29 ID - Law2014 ER - TY - JOUR AU - Li, B. AU - Dewey, C. N. PY - 2011 DA - 2011// TI - RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-323 DO - 10.1186/1471-2105-12-323 ID - Li2011 ER - TY - JOUR AU - Patro, R. AU - Mount, S. M. AU - Kingsford, C. PY - 2014 DA - 2014// TI - Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms JO - Nat Biotechnol VL - 32 UR - https://doi.org/10.1038/nbt.2862 DO - 10.1038/nbt.2862 ID - Patro2014 ER - TY - JOUR AU - Li, X. AU - Rouchka, E. C. AU - Brock, G. N. AU - Yan, J. AU - O'Toole, T. E. AU - Tieri, D. A. PY - 2018 DA - 2018// TI - A combined approach with gene-wise normalization improves the analysis of RNA-seq data in human breast cancer subtypes JO - PLoS One VL - 13 UR - https://doi.org/10.1371/journal.pone.0201813 DO - 10.1371/journal.pone.0201813 ID - Li2018 ER - TY - JOUR AU - Kvam, V. M. AU - Liu, P. AU - Si, Y. PY - 2012 DA - 2012// TI - A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data JO - Am J Bot VL - 99 UR - https://doi.org/10.3732/ajb.1100340 DO - 10.3732/ajb.1100340 ID - Kvam2012 ER - TY - JOUR AU - Rapaport, F. AU - Khanin, R. AU - Liang, Y. AU - Pirun, M. AU - Krek, A. AU - Zumbo, P. PY - 2013 DA - 2013// TI - Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-9-r95 DO - 10.1186/gb-2013-14-9-r95 ID - Rapaport2013 ER - TY - JOUR AU - Li, P. AU - Piao, Y. AU - Shon, H. S. AU - Ryu, K. H. PY - 2015 DA - 2015// TI - Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data JO - BMC Bioinformatics VL - 16 UR - https://doi.org/10.1186/s12859-015-0778-7 DO - 10.1186/s12859-015-0778-7 ID - Li2015 ER - TY - JOUR AU - Soneson, C. AU - Delorenzi, M. PY - 2013 DA - 2013// TI - A comparison of methods for differential expression analysis of RNA-seq data JO - BMC Bioinformatics VL - 14 UR - https://doi.org/10.1186/1471-2105-14-91 DO - 10.1186/1471-2105-14-91 ID - Soneson2013 ER - TY - JOUR AU - Seyednasrollah, F. AU - Laiho, A. AU - Elo, L. L. PY - 2015 DA - 2015// TI - Comparison of software packages for detecting differential expression in RNA-seq studies JO - Brief Bioinform VL - 16 UR - https://doi.org/10.1093/bib/bbt086 DO - 10.1093/bib/bbt086 ID - Seyednasrollah2015 ER - TY - JOUR AU - Zhang, Z. H. AU - Jhaveri, D. J. AU - Marshall, V. M. AU - Bauer, D. C. AU - Edson, J. AU - Narayanan, R. K. PY - 2014 DA - 2014// TI - A comparative study of techniques for differential expression analysis on RNA-Seq data JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0103207 DO - 10.1371/journal.pone.0103207 ID - Zhang2014 ER - TY - JOUR AU - Lin, Y. AU - Golovnina, K. AU - Chen, Z. X. AU - Lee, H. N. AU - Negron, Y. L. AU - Sultana, H. PY - 2016 DA - 2016// TI - Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster JO - BMC Genomics VL - 17 UR - https://doi.org/10.1186/s12864-015-2353-z DO - 10.1186/s12864-015-2353-z ID - Lin2016 ER - TY - JOUR AU - Tang, M. AU - Sun, J. AU - Shimizu, K. AU - Kadota, K. PY - 2015 DA - 2015// TI - Evaluation of methods for differential expression analysis on multi-group RNA-seq count data JO - BMC Bioinformatics VL - 16 UR - https://doi.org/10.1186/s12859-015-0794-7 DO - 10.1186/s12859-015-0794-7 ID - Tang2015 ER - TY - JOUR AU - Germain, P. L. AU - Vitriolo, A. AU - Adamo, A. AU - Laise, P. AU - Das, V. AU - Testa, G. PY - 2016 DA - 2016// TI - RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw448 DO - 10.1093/nar/gkw448 ID - Germain2016 ER - TY - JOUR AU - Maza, E. PY - 2016 DA - 2016// TI - In Papyro comparison of TMM (edgeR), RLE (DESeq2), and MRN normalization methods for a simple two-conditions-without-replicates RNA-Seq experimental design JO - Front Genet VL - 7 UR - https://doi.org/10.3389/fgene.2016.00164 DO - 10.3389/fgene.2016.00164 ID - Maza2016 ER - TY - JOUR AU - Costa-Silva, J. AU - Domingues, D. AU - Lopes, F. M. PY - 2017 DA - 2017// TI - RNA-Seq differential expression analysis: an extended review and a software tool JO - PLoS One VL - 12 UR - https://doi.org/10.1371/journal.pone.0190152 DO - 10.1371/journal.pone.0190152 ID - Costa-Silva2017 ER - TY - JOUR AU - Spies, D. AU - Renz, P. F. AU - Beyer, T. A. AU - Ciaudo, C. PY - 2019 DA - 2019// TI - Comparative analysis of differential gene expression tools for RNA sequencing time course data JO - Brief Bioinform VL - 20 UR - https://doi.org/10.1093/bib/bbx115 DO - 10.1093/bib/bbx115 ID - Spies2019 ER - TY - JOUR AU - Lun, A. T. AU - Chen, Y. AU - Smyth, G. K. PY - 2016 DA - 2016// TI - It's DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR JO - Methods Mol Biol VL - 1418 UR - https://doi.org/10.1007/978-1-4939-3578-9_19 DO - 10.1007/978-1-4939-3578-9_19 ID - Lun2016 ER - TY - JOUR AU - Consortium, M. AU - Shi, L. AU - Reid, L. H. AU - Jones, W. D. AU - Shippy, R. AU - Warrington, J. A. PY - 2006 DA - 2006// TI - The MicroArray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements JO - Nat Biotechnol VL - 24 UR - https://doi.org/10.1038/nbt1239 DO - 10.1038/nbt1239 ID - Consortium2006 ER - TY - JOUR AU - Wan, L. AU - Sun, F. PY - 2012 DA - 2012// TI - CEDER: accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq JO - IEEE/ACM Trans Comput Biol Bioinform VL - 9 UR - https://doi.org/10.1109/TCBB.2012.83 DO - 10.1109/TCBB.2012.83 ID - Wan2012 ER - TY - JOUR AU - Grossman, R. L. AU - Heath, A. P. AU - Ferretti, V. AU - Varmus, H. E. AU - Lowy, D. R. AU - Kibbe, W. A. PY - 2016 DA - 2016// TI - Toward a shared vision for Cancer genomic data JO - N Engl J Med VL - 375 UR - https://doi.org/10.1056/NEJMp1607591 DO - 10.1056/NEJMp1607591 ID - Grossman2016 ER - TY - JOUR AU - Robinson, M. D. AU - Smyth, G. K. PY - 2008 DA - 2008// TI - Small-sample estimation of negative binomial dispersion, with applications to SAGE data JO - Biostatistics VL - 9 UR - https://doi.org/10.1093/biostatistics/kxm030 DO - 10.1093/biostatistics/kxm030 ID - Robinson2008 ER - TY - JOUR AU - Li, X. AU - Gu, G. AU - Soliman, F. AU - Sanders, A. J. AU - Wang, X. AU - Liu, C. PY - 2018 DA - 2018// TI - The evaluation of durative transfusion of Endostar combined with chemotherapy in patients with advanced non-small cell lung cancer JO - Chemotherapy VL - 63 UR - https://doi.org/10.1159/000493098 DO - 10.1159/000493098 ID - Li2018 ER - TY - JOUR AU - Guo, Y. AU - Li, C. I. AU - Ye, F. AU - Shyr, Y. PY - 2013 DA - 2013// TI - Evaluation of read count based RNAseq analysis methods JO - BMC Genomics VL - 14 UR - https://doi.org/10.1186/1471-2164-14-S8-S2 DO - 10.1186/1471-2164-14-S8-S2 ID - Guo2013 ER - TY - JOUR AU - Soneson, C. AU - Robinson, M. D. PY - 2018 DA - 2018// TI - Bias, robustness and scalability in single-cell differential expression analysis JO - Nat Methods VL - 15 UR - https://doi.org/10.1038/nmeth.4612 DO - 10.1038/nmeth.4612 ID - Soneson2018 ER - TY - JOUR AU - Klein, A. M. AU - Mazutis, L. AU - Akartuna, I. AU - Tallapragada, N. AU - Veres, A. AU - Li, V. PY - 2015 DA - 2015// TI - Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells JO - Cell VL - 161 UR - https://doi.org/10.1016/j.cell.2015.04.044 DO - 10.1016/j.cell.2015.04.044 ID - Klein2015 ER - TY - JOUR AU - Usoskin, D. AU - Furlan, A. AU - Islam, S. AU - Abdo, H. AU - Lonnerberg, P. AU - Lou, D. PY - 2015 DA - 2015// TI - Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing JO - Nat Neurosci VL - 18 UR - https://doi.org/10.1038/nn.3881 DO - 10.1038/nn.3881 ID - Usoskin2015 ER - TY - JOUR AU - Zheng, C. AU - Zheng, L. AU - Yoo, J. K. AU - Guo, H. AU - Zhang, Y. AU - Guo, X. PY - 2017 DA - 2017// TI - Landscape of infiltrating T cells in liver Cancer revealed by single-cell sequencing JO - Cell VL - 169 UR - https://doi.org/10.1016/j.cell.2017.05.035 DO - 10.1016/j.cell.2017.05.035 ID - Zheng2017 ER - TY - JOUR AU - Myers, J. S. AU - Lersner, A. K. AU - Robbins, C. J. AU - Sang, Q. X. PY - 2015 DA - 2015// TI - Differentially expressed genes and signature pathways of human prostate Cancer JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0145322 DO - 10.1371/journal.pone.0145322 ID - Myers2015 ER - TY - JOUR AU - Kharchenko, P. V. AU - Silberstein, L. AU - Scadden, D. T. PY - 2014 DA - 2014// TI - Bayesian approach to single-cell differential expression analysis JO - Nat Methods VL - 11 UR - https://doi.org/10.1038/nmeth.2967 DO - 10.1038/nmeth.2967 ID - Kharchenko2014 ER - TY - JOUR AU - Finak, G. AU - McDavid, A. AU - Yajima, M. AU - Deng, J. AU - Gersuk, V. AU - Shalek, A. K. PY - 2015 DA - 2015// TI - MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0844-5 DO - 10.1186/s13059-015-0844-5 ID - Finak2015 ER - TY - JOUR AU - Nabavi, S. AU - Schmolze, D. AU - Maitituoheti, M. AU - Malladi, S. AU - Beck, A. H. PY - 2016 DA - 2016// TI - EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes JO - Bioinformatics VL - 32 UR - https://doi.org/10.1093/bioinformatics/btv634 DO - 10.1093/bioinformatics/btv634 ID - Nabavi2016 ER - TY - JOUR AU - Miao, Z. AU - Deng, K. AU - Wang, X. AU - Zhang, X. PY - 2018 DA - 2018// TI - DEsingle for detecting three types of differential expression in single-cell RNA-seq data JO - Bioinformatics VL - 34 UR - https://doi.org/10.1093/bioinformatics/bty332 DO - 10.1093/bioinformatics/bty332 ID - Miao2018 ER - TY - JOUR AU - Jaakkola, M. K. AU - Seyednasrollah, F. AU - Mehmood, A. AU - Elo, L. L. PY - 2017 DA - 2017// TI - Comparison of methods to detect differentially expressed genes between single-cell populations JO - Brief Bioinform VL - 18 ID - Jaakkola2017 ER - TY - JOUR AU - Wang, T. AU - Li, B. AU - Nelson, C. E. AU - Nabavi, S. PY - 2019 DA - 2019// TI - Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data JO - BMC Bioinformatics VL - 20 UR - https://doi.org/10.1186/s12859-019-2599-6 DO - 10.1186/s12859-019-2599-6 ID - Wang2019 ER - TY - JOUR AU - Robinson, M. D. AU - McCarthy, D. J. AU - Smyth, G. K. PY - 2010 DA - 2010// TI - edgeR: a bioconductor package for differential expression analysis of digital gene expression data JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp616 DO - 10.1093/bioinformatics/btp616 ID - Robinson2010 ER - TY - JOUR AU - Keene, O. N. AU - Jones, M. R. AU - Lane, P. W. AU - Anderson, J. PY - 2007 DA - 2007// TI - Analysis of exacerbation rates in asthma and chronic obstructive pulmonary disease: example from the TRISTAN study JO - Pharm Stat VL - 6 UR - https://doi.org/10.1002/pst.250 DO - 10.1002/pst.250 ID - Keene2007 ER - TY - JOUR AU - Zhu, H. AU - Lakkis, H. PY - 2014 DA - 2014// TI - Sample size calculation for comparing two negative binomial rates JO - Stat Med VL - 33 UR - https://doi.org/10.1002/sim.5947 DO - 10.1002/sim.5947 ID - Zhu2014 ER - TY - STD TI - Li X, Wu D, Cooper NGF, Rai SN. Sample size calculations for the differential expression analysis of RNA-seq data using a negative binomial regression model. Stat Appl Genet Mol Biol. 2019;18(1). https://doi.org/10.1515/sagmb-2018-0021. ID - ref66 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 B VL - 57 ID - Benjamini1995 ER - TY - JOUR AU - Robinson, M. D. AU - Smyth, G. K. PY - 2007 DA - 2007// TI - Moderated statistical tests for assessing differences in tag abundance JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm453 DO - 10.1093/bioinformatics/btm453 ID - Robinson2007 ER - TY - JOUR AU - Yu, D. AU - Huber, W. AU - Vitek, O. PY - 2013 DA - 2013// TI - Shrinkage estimation of dispersion in negative binomial models for RNA-seq experiments with small sample size JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt143 DO - 10.1093/bioinformatics/btt143 ID - Yu2013 ER - TY - JOUR AU - Schurch, N. J. AU - Schofield, P. AU - Gierlinski, M. AU - Cole, C. AU - Sherstnev, A. AU - Singh, V. PY - 2016 DA - 2016// TI - How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? JO - RNA VL - 22 UR - https://doi.org/10.1261/rna.053959.115 DO - 10.1261/rna.053959.115 ID - Schurch2016 ER -