DEGseq swMATH ID: 7998 Software Authors: Likun Wang; Zhixing Feng; Xi Wang; Xiaowo Wang; Xuegong Zhang Description: DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. High-throughput RNA sequencing (RNA-seq) is rapidly emerging as a major quantitative transcriptome profiling platform. Here, we present DEGseq, an R package to identify differentially expressed genes or isoforms for RNA-seq data from different samples. In this package, we integrated three existing methods, and introduced two novel methods based on MA-plot to detect and visualize gene expression difference. Homepage: http://bioinfo.au.tsinghua.edu.cn/software/degseq/ Related Software: edgeR; Bioconductor; DEseq; R; BaySeq; Voom; DESeq2; RUVseq; FindPeaks; BayesPeak; robCompositions; NeatMap; betapart; INMEX; HMP; MetamicrobiomeR; MicrobiomeAnalyst; MDSINE; pplacer; UrQt Cited in: 9 Publications all top 5 Cited by 67 Authors 2 Li, Chung-I 2 Shyr, Yu 1 Aransay, Ana M. 1 Bickel, Peter John 1 Boice, John D. jun. 1 Boley, Nathan 1 Bonafede, Elisabetta 1 Brown, James Bentley 1 Chen, Mengjie 1 Chen, Yunshun 1 Chung, Dongjun 1 Collado Torres, Leonardo 1 Dadaneh, Siamak Zamani 1 Datta, Somnath 1 Datta, Susmita 1 Du, Ruofei 1 Dudoit, Sandrine 1 Fang, Zhide 1 Frazee, Alyssa C. 1 Ghosh, Debashis 1 Gill, Ryan S. 1 Girirajan, Santhosh 1 Hackenberg, Michael 1 Hou, Lin 1 Hsueh, Hueymiin 1 Hu, Yijuan 1 Huang, Haiyan 1 Jaffe, Andrew E. 1 Jeong, Seongmun 1 Keles, Sunduz 1 Langmead, Ben 1 Leek, Jeffrey T. 1 Liu, MingTe 1 Liu, Peng 1 Liu, Qi 1 Lorenz, Douglas J. 1 Lun, Aaron T. L. 1 Mau, Yu-Lin 1 Mitra, Ritendranath 1 Nettleton, Dan 1 Ngai, John 1 Petersen, Ashley 1 Picard, Franck 1 Qian, Xiaoning 1 Riebler, Andrea 1 Risso, Davide 1 Robin, Stéphane 1 Robinson, Mark D. 1 Rodríguez-Ezpeleta, Naiara 1 Salzman, Julia 1 Seshan, Venkatraman E. 1 Si, Yaqing 1 Smyth, Gordon K. 1 Speed, Terence Paul 1 Su, Pei-Fang 1 Sun, Wei 1 Tan, Kean Ming 1 Viroli, Cinzia 1 Witten, Daniela M. 1 Xia, Yinglin 1 Xiong, Hao 1 Yang, Tae Young 1 Zhang, Kui 1 Zhang, Qi 1 Zhao, Hongyu 1 Zhi, Degui 1 Zhou, Mingyuan all top 5 Cited in 7 Serials 2 Statistical Applications in Genetics and Molecular Biology 1 Biometrics 1 Journal of the American Statistical Association 1 Statistics & Probability Letters 1 Journal of the Korean Statistical Society 1 ICSA Book Series in Statistics 1 Frontiers in Probability and the Statistical Sciences Cited in 4 Fields 7 Statistics (62-XX) 6 Biology and other natural sciences (92-XX) 1 General and overarching topics; collections (00-XX) 1 Numerical analysis (65-XX) Citations by Year