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DiPhiSeq  

Robust Tests for Differential Dispersion and Differential Expression in RNA-Sequencing Data
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("DiPhiSeq", "0.2.0")



Attach the package and use:
library("DiPhiSeq")
Maintained by
Jun Li
[Scholar Profile | Author Map]
First Published: 2018-06-14
Latest Update: 2018-10-24
Description:
Implements the algorithm described in Jun Li and Alicia T. Lamere, "DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes" (Unpublished). Detects not only genes that show different average expressions ("differential expression", DE), but also genes that show different diversities of expressions in different groups ("differentially dispersed", DD). DD genes can be important clinical markers. 'DiPhiSeq' uses a redescending penalty on the quasi-likelihood function, and thus has superior robustness against outliers and other noise. Updates from version 0.1.0: (1) Added the option of using adaptive initial value for phi. (2) Added a function for estimating the proportion of outliers in the data. (3) Modified the input parameter names for clarity, and modified the output format for the main function.
How to cite:
Jun Li (2018). DiPhiSeq: Robust Tests for Differential Dispersion and Differential Expression in RNA-Sequencing Data. R package version 0.2.0, https://cran.r-project.org/web/packages/DiPhiSeq. Accessed 29 Mar. 2025.
Previous versions and publish date:
0.1.0 (2018-06-14 21:00)
Other packages that cited DiPhiSeq R package
View DiPhiSeq citation profile
Other R packages that DiPhiSeq depends, imports, suggests or enhances
Complete documentation for DiPhiSeq
Functions, R codes and Examples using the DiPhiSeq R package
Some associated functions: diphiseq . example_data . outprop . robnb . robtest . 
Some associated R codes: data.R . diphiseq.R . robstat.R . robtest.R .  Full DiPhiSeq package functions and examples
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