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.

References in zbMATH (referenced in 11 articles )

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  1. Dadaneh, Siamak Zamani; Qian, Xiaoning; Zhou, Mingyuan: BNP-seq: Bayesian nonparametric differential expression analysis of sequencing count data (2018)
  2. Xia, Yinglin; Sun, Jun; Chen, Ding-Geng: Statistical analysis of microbiome data with R (2018)
  3. Yang, Tae Young; Jeong, Seongmun: Controlling the false-discovery rate by procedures adapted to the length bias of RNA-seq (2018)
  4. Su, Pei-Fang; Mau, Yu-Lin; Guo, Yan; Li, Chung-I; Liu, Qi; Boice, John D.; Shyr, Yu: Bivariate Poisson models with varying offsets: an application to the paired mitochondrial DNA dataset (2017)
  5. Bonafede, Elisabetta; Picard, Franck; Robin, Stéphane; Viroli, Cinzia: Modeling overdispersion heterogeneity in differential expression analysis using mixtures (2016)
  6. Li, Chung-I; Shyr, Yu: Sample size calculation based on generalized linear models for differential expression analysis in RNA-seq data (2016)
  7. Datta, Somnath (ed.); Nettleton, Dan (ed.): Statistical analysis of next generation sequencing data (2014)
  8. Liu, MingTe; Hsueh, Huey-Miin: Exact tests of the superiority under the Poisson distribution (2013)
  9. Rodríguez-Ezpeleta, Naiara (ed.); Hackenberg, Michael (ed.); Aransay, Ana M. (ed.): Bioinformatics for high throughput sequencing (2012)
  10. Wang, Likun; Feng, Zhixing; Wang, Xi; Wang, Xiaowo; Zhang, Xuegong: Degseq: an R package for identifying differentially expressed genes from RNA-seq data (2010) ioport
  11. Zhu, Lihua J.; Gazin, Claude; Lawson, Nathan D.; Pagès, Hervé; Lin, Simon M.; Lapointe, David S.; Green, Michael R.: Chippeakanno: a bioconductor package to annotate chip-seq and chip-chip data (2010) ioport