Other packages > Find by keyword >

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]
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 06 May. 2025.
Previous versions and publish date:
1.0 (2014-05-15 01:12)
Other packages that cited DoubleExpSeq R package
View DoubleExpSeq citation profile
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
Downloads during the last 30 days
04/0604/0704/0804/0904/1004/1104/1204/1304/1404/1504/1604/1704/1804/1904/2004/2104/2204/2304/2404/2504/2604/2704/2804/2904/3005/0105/0205/0305/0405/05Downloads for DoubleExpSeq051015202530TrendBars

Today's Hot Picks in Authors and Packages

r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
tashu  
Analysis and Prediction of Bicycle Rental Amount
Provides functions for analyzing citizens' bicycle usage pattern and predicting rental amount on spe ...
Download / Learn more Package Citations See dependency  
rotations  
Working with Rotation Data
Tools for working with rotational data, including simulation from the most commonly used distributi ...
Download / Learn more Package Citations See dependency  
tbrf  
Time-Based Rolling Functions
Provides rolling statistical functions based on date and time windows instead of n-lagged observatio ...
Download / Learn more Package Citations See dependency  
simfam  
Simulate and Model Family Pedigrees with Structured Founders
The focus is on simulating and modeling families with founders drawn from a structured population (f ...
Download / Learn more Package Citations See dependency  
HuraultMisc  
Guillem Hurault Functions' Library
Contains various functions for data analysis, notably helpers and diagnostics for Bayesian modelling ...
Download / Learn more Package Citations See dependency  

24,205

R Packages

207,311

Dependencies

65,312

Author Associations

24,206

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA