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DoubleExpSeq  

Differential Exon Usage Test for RNA-Seq Data via Empirical Bayes Shrinkage of the Dispersion Parameter
View on CRAN: Click here


Download and install DoubleExpSeq package within the R console
Install from CRAN:
install.packages("DoubleExpSeq")

Install from Github:
library("remotes")
install_github("cran/DoubleExpSeq")

Install by package version:
library("remotes")
install_version("DoubleExpSeq", "1.1")



Attach the package and use:
library("DoubleExpSeq")
Maintained by
Sean Ruddy
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-05-15
Latest Update: 2015-09-04
Description:
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.
How to cite:
Sean Ruddy (2014). DoubleExpSeq: Differential Exon Usage Test for RNA-Seq Data via Empirical Bayes Shrinkage of the Dispersion Parameter. R package version 1.1, https://cran.r-project.org/web/packages/DoubleExpSeq. Accessed 21 Nov. 2024.
Previous versions and publish date:
1.0 (2014-05-15 01:12)
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Other R packages that DoubleExpSeq depends, imports, suggests or enhances
Complete documentation for DoubleExpSeq
Functions, R codes and Examples using the DoubleExpSeq R package
Some associated functions: DB.MAPlot . DBGLM1 . DoubleExpSeq-package . EstimateDEBDisp . EstimateWEBDisp . counts . exon . groups . offsets . optimPlot . 
Some associated R codes: DB.MAPlot.R . DBGLM1.R . DoubleExpSeq-internal.R . EstimateDEBDisp.R . EstimateWEBDisp.R . optimPlot.R .  Full DoubleExpSeq package functions and examples
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