CRAN/E | DiPhiSeq

DiPhiSeq

Robust Tests for Differential Dispersion and Differential Expression in RNA-Sequencing Data

Installation

About

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Li and Alicia T. Lamere, "DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes" (Unpublished).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.

Key Metrics

Version 0.2.0
R ≥ 3.1.0
Published 2018-10-24 2005 days ago
Needs compilation? no
License GPL-3
CRAN checks DiPhiSeq results

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Maintainer

Maintainer

Jun Li

jun.li@nd.edu

Authors

Jun Li

aut / cre

Alicia T. Lamere

aut

Material

Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

DiPhiSeq archive

Depends

R ≥ 3.1.0

Imports

stats ≥ 3.1.0