Differential Exon Usage Test for RNA-Seq Data via Empirical Bayes Shrinkage of the Dispersion Parameter
Exon Inclusion Counts
Plots Log-Fold Change versus Log-Concentration for Inclusion/Exclusion...
Double Binomial Generalized Linear Model with Shrinkage of the Dispers...
DoubleExpSeq is a package with application to RNA-Seq experiments that...
DEB-Seq: Empirical Bayes Estimates of Dispersion for a Double Binomial...
WEB-Seq: Weighted Likelihood Empirical Bayes Estimates of Dispersion f...
Group Structure of the Toy Data Set
Exon Total Counts
Plot the WEB-Seq Maximum Likelihood Solution for the Weight Parameter ...
Differential exon usage test for RNA-Seq data via an empirical Bayes shrinkage method for the dispersion parameter the utilizes inclusion-exclusion data to analyze the propensity to skip an exon across groups. The input data consists of two matrices where each row represents an exon and the columns represent the biological samples. The first matrix is the count of the number of reads expressing the exon for each sample. The second matrix is the count of the number of reads that either express the exon or explicitly skip the exon across the samples, a.k.a. the total count matrix. Dividing the two matrices yields proportions representing the propensity to express the exon versus skipping the exon for each sample.