Ning Leng, John A Dawson and Christina Kendziorski
University of Wisconsin Madison
Contact email: firstname.lastname@example.org, email@example.com
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).
devel = "http://bioconductor.org/packages/2.13/bioc"
biocLite("EBSeq", siteRepos = devel)
Leng, N., J.A. Dawson, J.A. Thomson, V. Ruotti, A.I. Rissman, B.M.G. Smits, J.D. Haag, M.N. Gould, R.M. Stewart, and C. Kendziorski. EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments, Bioinformatics, 2013. Paper
Li, B., V. Ruotti, R.M. Stewart, J.A. Thomson, and C. Dewey. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26(4): 493-500, 2010.
A bug in QuantileNorm() function which might cause overflow was fixed.
The documentation files are improved. A new feature is implemented in the GetMultiFC function - providing the posterior fold change for each pair of comparison.
A new function GetNormalizedMat is added. The function could provide normalized matrix for visualization.
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.
Welcome to join our EBSeq users' group