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PDEGEM

PDEGEM

PDEGEM (Positional Dependent Energy Guided Expression Model ) is a tool to estimate transcript abundance and isoform expression in RNA-seq data. The PDEGEM algorithm uses the Positional Dependent Nearest Neighborhood (PDNN) based technique to model the distribution of reads.

Topic

RNA-seq; RNA-seq; RNA

Details

  • Operation: RNA-Seq analysis; Regression analysis
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Credit: The National Natural Science Foundation of China, the National Key Basic Research Project of China.
  • Contact: Minghua Deng dengmh _at_ math.pku.edu.cn | Yuchao Xia xiayuchao _at_ pku.edu.cn
  • Collection: -

Publications

Xia Y, Wang F, Qian M, Qin Z, Deng M "PDEGEM: Modeling non-uniform read distribution in RNA-Seq data." BMC Med Genomics 2015 https://doi.org/10.1186/1755-8794-8-S2-S14
PMID: 26044773
PMCID: PMC4460722


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