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

  • 2014-9-4: In EBSeq 1.5.4, an extra numerical approximation step is implemented in EBMultiTest() function to avoid underflow. The underflow is likely due to large number of samples. A bug in EBMultiTest() is fixed. The bug will cause error when there is exactly 1 gene/isoform that needs numerical approximation.
  • 2014-6-24 EBSeqHMM is released. EBSeq-HMM: A Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments
  • 2014-6-5 In EBSeq 1.5.3, a bug is fixed. The bug may generate NA FC estimates when there are no replicates.
  • 2014-5-22 In EBSeq 1.5.2, numerical approximations are implemented to deal with underflow. The underflow is likely due to large number of samples.
  • 2014-1-30 In EBSeq 1.3.3, the default setting of EBTest function will remove low expressed genes (genes whose 75th quantile of normalized counts is less than 10) before identifying DE genes. These two thresholds can be changed in EBTest function. We found that low expressed genes are more easily to be affected by noises. Removing these genes prior to downstream analyses can improve the model fitting and reduce impacts of noisy genes (e.g. genes with outliers).
  • 2013-06-03 EBSeq is currently available at Bioconductor (BioC-dev). EBSeq Bioconductor page
  • A bug in QuantileNorm() function which might cause overflow was fixed.
  • 2013-03-19 EBSeq Interface codes are released!
  • 2013-03-15 EBSeq Galaxy wrappers are released at EBSeq Galaxy tool shed. An user friendly interface of EBSeq is coming soon!
  • 2013-02-21 EBSeq Paper is published at Bioinformatics.
  • 2013-01-16 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

  • 2013-01-07 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

  • 2012-11-29 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