EBSeq

EBSeq is a software tool for identifying differentially expressed (DE) isoforms and genes from RNA-seq data when comparing two or more biological conditions. It addresses the limitations of existing count-based methods, which need to be better suited for handling the varying uncertainty in isoform expression estimates. By employing empirical Bayesian methods, EBSeq provides improved power and performance in identifying DE isoforms while proving to be a robust approach for identifying DE genes.

Topic

Statistics and probability;Gene expression;Molecular interactions, pathways and networks;RNA-Seq

Detail

  • Operation: Gene expression clustering;RNA-seq time series data analysis;Differential gene expression analysis

  • Software interface: Command-line user interface, Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free of charge with limitations

  • Version name: 2.2.0

  • Credit: NIH, NIEHS, The Morgridge Institute for Research.

  • Input: Gene expression profile [Gene expression report format] [Textual format]

  • Output: Plot [Textual format] [Image format], Report [Textual format] [Image format]

  • Contact: Xiuyu Ma watsonforfun at gmail.com, Ning Leng lengning1@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.
  • Leng N, et al. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. 2013; 29:1035-43. doi: 10.1093/bioinformatics/btt087
  • https://doi.org/10.1093/bioinformatics/btt087
  • PMID: 23428641
  • PMC: PMC3624807

Download and documentation

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