DoubleExpSeq: Differential Exon Usage Test for RNA-Seq Data via Empirical Bayes Shrinkage of the Dispersion Parameter
Version 1.1

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.

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AuthorSean Ruddy
Date of publication2015-09-04 09:25:45
MaintainerSean Ruddy <s.ruddy@yahoo.com>
LicenseGPL-3
Version1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DoubleExpSeq")

Man pages

counts: Exon Inclusion Counts
DBGLM1: Double Binomial Generalized Linear Model with Shrinkage of...
DB.MAPlot: Plots Log-Fold Change versus Log-Concentration for...
DoubleExpSeq-package: DoubleExpSeq is a package with application to RNA-Seq...
EstimateDEBDisp: DEB-Seq: Empirical Bayes Estimates of Dispersion for a Double...
EstimateWEBDisp: WEB-Seq: Weighted Likelihood Empirical Bayes Estimates of...
exon: Toy Exon Inclusion and Total Counts Used for Examples
groups: Group Structure of the Toy Data Set
offsets: Exon Total Counts
optimPlot: Plot the WEB-Seq Maximum Likelihood Solution for the Weight...

Functions

DB.MAPlot Man page Source code
DBGLM1 Man page Source code
DBS Source code
DBSplitIntoGroups Source code
DoubleExpSeq Man page
DoubleExpSeq-package Man page
EstimateDEBDisp Man page Source code
EstimateWEBDisp Man page Source code
Hessian Source code
Hessian.gamma.bq Source code
counts Man page
eta Source code
exon Man page
gr.nlgbp Source code
gr.nlgbp.gamma.bq Source code
groups Man page
nll.gbp Source code
nll.gbp.delta2 Source code
nll.gbp.gamma.bq Source code
nll.gbp2 Source code
offsets Man page
optimPlot Man page Source code
psi Source code
rho Source code

Files

NAMESPACE
data
data/exon.RData
R
R/DoubleExpSeq-internal.R
R/DBGLM1.R
R/optimPlot.R
R/DB.MAPlot.R
R/EstimateDEBDisp.R
R/EstimateWEBDisp.R
MD5
DESCRIPTION
man
man/DoubleExpSeq-package.Rd
man/EstimateDEBDisp.Rd
man/offsets.Rd
man/optimPlot.Rd
man/EstimateWEBDisp.Rd
man/counts.Rd
man/groups.Rd
man/DBGLM1.Rd
man/DB.MAPlot.Rd
man/exon.Rd
DoubleExpSeq documentation built on May 20, 2017, 3:16 a.m.