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.

Author | Sean Ruddy |

Date of publication | 2015-09-04 09:25:45 |

Maintainer | Sean Ruddy <s.ruddy@yahoo.com> |

License | GPL-3 |

Version | 1.1 |

**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...

DoubleExpSeq

DoubleExpSeq/NAMESPACE

DoubleExpSeq/data

DoubleExpSeq/data/exon.RData

DoubleExpSeq/R

DoubleExpSeq/R/DoubleExpSeq-internal.R
DoubleExpSeq/R/DBGLM1.R
DoubleExpSeq/R/optimPlot.R
DoubleExpSeq/R/DB.MAPlot.R
DoubleExpSeq/R/EstimateDEBDisp.R
DoubleExpSeq/R/EstimateWEBDisp.R
DoubleExpSeq/MD5

DoubleExpSeq/DESCRIPTION

DoubleExpSeq/man

DoubleExpSeq/man/DoubleExpSeq-package.Rd
DoubleExpSeq/man/EstimateDEBDisp.Rd
DoubleExpSeq/man/offsets.Rd
DoubleExpSeq/man/optimPlot.Rd
DoubleExpSeq/man/EstimateWEBDisp.Rd
DoubleExpSeq/man/counts.Rd
DoubleExpSeq/man/groups.Rd
DoubleExpSeq/man/DBGLM1.Rd
DoubleExpSeq/man/DB.MAPlot.Rd
DoubleExpSeq/man/exon.Rd
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