EBSeq: An R package for RNA-Seq Differential Expression Analysis

Ning Leng, John A Dawson and Christina Kendziorski

University of Wisconsin Madison

Contact email: nleng@wisc.edu, kendzior@biostat.wisc.edu






R/EBSeq is an R package for identifying genes and isoforms differentially expressed (DE) across two or more biological conditions in an RNA-seq experiment. Details can be found in Leng et al., 2013. The R/EBSeq package may be downloaded below. A vignette is also available there. It provides the syntax required for identifying DE genes and isoforms in a two-group RNA-seq experiment as well for identifying DE genes across more than two conditions (as noted in the vignette, the commands for identifying DE isoforms across more than two conditions are the same as those required for gene-level analysis).

Installation

Vignette

EBSeq User Interface

EBSeq Galaxy toolshed

RSEM-EBSeq pipeline

EBSeq is now coupled with RSEM (Li et al. 2010) so that RSEM may be used to quantify expression, and EBSeq may follow to identify DE genes and isoforms. For more details, see RSEM-EBSeq pipeline.

References

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Updates

  • 06/03/2013 EBSeq is currently available at Bioconductor (BioC-dev). EBSeq Bioconductor page
  • A bug in QuantileNorm() function which might cause overflow was fixed.
  • 03/19/2013 EBSeq Interface codes are released!
  • 03/15/2013 EBSeq Galaxy wrappers are released at EBSeq Galaxy tool shed. An user friendly interface of EBSeq is coming soon!
  • 02/21/2013 EBSeq Paper is published at Bioinformatics.
  • 01/16/2013 EBSeq 1.1.6 is released.

    The documentation files are improved. A new feature is implemented in the GetMultiFC function - providing the posterior fold change for each pair of comparison.

    EBSeq_1.1.6.tar.gz

    EBSeq_1.1.6.zip

  • 01/07/2013 EBSeq 1.1.5 is released with RSEM 1.2.2.

    A new function GetNormalizedMat is added. The function could provide normalized matrix for visualization.

    EBSeq_1.1.5.tar.gz

    EBSeq_1.1.5.zip

  • 11/29/2012 EBSeq 1.1.4 is released with RSEM 1.2.1.

    EBSeq_1.1.4.tar.gz

    EBSeq_1.1.4.zip

  • EBSeq is running on a local version of Galaxy in the Thomson Lab; soon it will be released to a public Galaxy site.
  • EBSeq is now coupled with RSEM (Li et al. 2010) so that RSEM may be used to quantify expression, and EBSeq may follow to identify DE genes and isoforms. See RSEM-EBSeq pipeline.

  • EBSeq Users group

    Welcome to join our EBSeq users' group