@article{chu2012review, title={RNA sequencing: platform selection, experimental design, and data interpretation}, author={Chu, Yongjun and Corey, David R}, journal={Nucleic acid therapeutics}, volume={22}, number={4}, pages={271--274}, year={2012}, publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA} } @article{trapnell2012tophat, title={Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks}, author={Trapnell, Cole and Roberts, Adam and Goff, Loyal and Pertea, Geo and Kim, Daehwan and Kelley, David R and Pimentel, Harold and Salzberg, Steven L and Rinn, John L and Pachter, Lior}, journal={Nature protocols}, volume={7}, number={3}, pages={562}, year={2012}, publisher={Nature Publishing Group} } @article{dobin2013star, title={STAR: ultrafast universal RNA-seq aligner}, author={Dobin, Alexander and Davis, Carrie A and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R}, journal={Bioinformatics}, volume={29}, number={1}, pages={15--21}, year={2013}, publisher={Oxford University Press} } @article{liao2013subread, title={The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote}, author={Liao, Yang and Smyth, Gordon K and Shi, Wei}, journal={Nucleic acids research}, volume={41}, number={10}, pages={e108--e108}, year={2013}, publisher={Oxford University Press} } @article{pertea2016hisat, title={Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown}, author={Pertea, Mihaela and Kim, Daehwan and Pertea, Geo M and Leek, Jeffrey T and Salzberg, Steven L}, journal={Nature protocols}, volume={11}, number={9}, pages={1650}, year={2016}, publisher={Nature Publishing Group} } @article{baruzzo2017aligners, title={Simulation-based comprehensive benchmarking of RNA-seq aligners}, author={Baruzzo, Giacomo and Hayer, Katharina E and Kim, Eun Ji and Di Camillo, Barbara and FitzGerald, Garret A and Grant, Gregory R}, journal={Nature methods}, volume={14}, number={2}, pages={135}, year={2017}, publisher={Nature Publishing Group} } @article{li2011rsem, title={RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome}, author={Li, Bo and Dewey, Colin N}, journal={BMC bioinformatics}, volume={12}, number={1}, pages={323}, year={2011}, publisher={BioMed Central} } @article{bray2016kallisto, title={Near-optimal probabilistic RNA-seq quantification}, author={Bray, Nicolas L and Pimentel, Harold and Melsted, P{\'a}ll and Pachter, Lior}, journal={Nature biotechnology}, volume={34}, number={5}, pages={525}, year={2016}, publisher={Nature Publishing Group} } @article{liao2013featurecounts, title={featureCounts: an efficient general purpose program for assigning sequence reads to genomic features}, author={Liao, Yang and Smyth, Gordon K and Shi, Wei}, journal={Bioinformatics}, volume={30}, number={7}, pages={923--930}, year={2013}, publisher={Oxford University Press} } @article{anders2015htseq, title={HTSeq—a Python framework to work with high-throughput sequencing data}, author={Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang}, journal={Bioinformatics}, volume={31}, number={2}, pages={166--169}, year={2015}, publisher={Oxford University Press} } @article{anders2013deseq, title={Count-based differential expression analysis of RNA sequencing data using R and Bioconductor}, author={Anders, Simon and McCarthy, Davis J and Chen, Yunshun and Okoniewski, Michal and Smyth, Gordon K and Huber, Wolfgang and Robinson, Mark D}, journal={Nature protocols}, volume={8}, number={9}, pages={1765}, year={2013}, publisher={Nature Publishing Group} } @article{love2014deseq2, title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2}, author={Love, Michael I and Huber, Wolfgang and Anders, Simon}, journal={Genome biology}, volume={15}, number={12}, pages={550}, year={2014}, publisher={BioMed Central} } @article{hardcastle2010bayseq, title={baySeq: empirical Bayesian methods for identifying differential expression in sequence count data}, author={Hardcastle, Thomas J and Kelly, Krystyna A}, journal={BMC bioinformatics}, volume={11}, number={1}, pages={422}, year={2010}, publisher={BioMed Central} } @article{law2014voom, title={voom: Precision weights unlock linear model analysis tools for RNA-seq read counts}, author={Law, Charity W and Chen, Yunshun and Shi, Wei and Smyth, Gordon K}, journal={Genome biology}, volume={15}, number={2}, pages={R29}, year={2014}, publisher={BioMed Central} } @article{ritchie2015limma, title={limma powers differential expression analyses for RNA-sequencing and microarray studies}, author={Ritchie, Matthew E and Phipson, Belinda and Wu, Di and Hu, Yifang and Law, Charity W and Shi, Wei and Smyth, Gordon K}, journal={Nucleic acids research}, volume={43}, number={7}, pages={e47--e47}, year={2015}, publisher={Oxford University Press} } @article{guo2013diffevaluation, title={Evaluation of read count based RNAseq analysis methods}, author={Guo, Yan and Li, Chung-I and Ye, Fei and Shyr, Yu}, journal={BMC genomics}, volume={14}, number={8}, pages={S2}, year={2013}, publisher={BioMed Central} } @article{rapaport2013comprehensive, title={Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data}, author={Rapaport, Franck and Khanin, Raya and Liang, Yupu and Pirun, Mono and Krek, Azra and Zumbo, Paul and Mason, Christopher E and Socci, Nicholas D and Betel, Doron}, journal={Genome biology}, volume={14}, number={9}, pages={3158}, year={2013}, publisher={BioMed Central} } @article{robertson2010transabyss, title={De novo assembly and analysis of RNA-seq data}, author={Robertson, Gordon and Schein, Jacqueline and Chiu, Readman and Corbett, Richard and Field, Matthew and Jackman, Shaun D and Mungall, Karen and Lee, Sam and Okada, Hisanaga Mark and Qian, Jenny Q and others}, journal={Nature methods}, volume={7}, number={11}, pages={909}, year={2010}, publisher={Nature Publishing Group} } @article{haas2013trinity, title={De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis}, author={Haas, Brian J and Papanicolaou, Alexie and Yassour, Moran and Grabherr, Manfred and Blood, Philip D and Bowden, Joshua and Couger, Matthew Brian and Eccles, David and Li, Bo and Lieber, Matthias and others}, journal={Nature protocols}, volume={8}, number={8}, pages={1494}, year={2013}, publisher={Nature Publishing Group} } @article{schulz2012oases, title={Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels}, author={Schulz, Marcel H and Zerbino, Daniel R and Vingron, Martin and Birney, Ewan}, journal={Bioinformatics}, volume={28}, number={8}, pages={1086--1092}, year={2012}, publisher={Oxford University Press} } @article{xie2014soapdenovo, title={SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads}, author={Xie, Yinlong and Wu, Gengxiong and Tang, Jingbo and Luo, Ruibang and Patterson, Jordan and Liu, Shanlin and Huang, Weihua and He, Guangzhu and Gu, Shengchang and Li, Shengkang and others}, journal={Bioinformatics}, volume={30}, number={12}, pages={1660--1666}, year={2014}, publisher={Oxford University Press} } @inproceedings{zhao2011optimizing, title={Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study}, author={Zhao, Qiong-Yi and Wang, Yi and Kong, Yi-Meng and Luo, Da and Li, Xuan and Hao, Pei}, booktitle={BMC bioinformatics}, volume={12}, number={14}, pages={S2}, year={2011}, organization={BioMed Central} } @incollection{djebali2017pipeline, title={Bioinformatics pipeline for transcriptome sequencing analysis}, author={Djebali, Sarah and Wucher, Valentin and Foissac, Sylvain and Hitte, Christophe and Corre, Erwan and Derrien, Thomas}, booktitle={Enhancer RNAs}, pages={201--219}, year={2017}, publisher={Springer} }