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IntEREst

IntEREst

IntEREst is an R tool to analyze Intron-Exon Retention in RNA-seq data sets. The IntEREst algorithm can analyze both annotated and non-annotated retention events. The IntEREst algorithm uses statistical methods, modified from DESeq2, edgeR, and DEXSeq R packages and supports single and multiple cores.

Topic

RNA-seq; Sequencing

Details

  • Operation: Alignment; Splicing model analysis; Differential protein expression analysis; Standardisation and normalisation
  • Input: BAM
  • Output: -
  • Software interface: Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v2
  • Cost: Free
  • Version name: 1.10.0
  • Maturity: Stable
  • Credit: Academy of Finland, Sigrid Júselius Foundation, University of Helsinki Viikki Doctoral Programme in Molecular Biosciences.
  • Contact: Oghabian A Ali.Oghabian _at_ Helsinki.Fi | Frilander MJ Mikko.Frilander _at_ helsinki.fi
  • Collection: BioConductor

Publications

Oghabian A, Greco D, Frilander MJ "IntEREst: intron-exon retention estimator." BMC Bioinformatics. 2018 Apr 11;19(1):130. https://doi.org/10.1186/s12859-018-2122-5
PMID: 29642843
PMCID: PMC5896110


Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590


Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600


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