Other packages > Find by keyword >

DEGRE  

Inferring Differentially Expressed Genes using Generalized Linear Mixed Models
View on CRAN: Click here


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

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

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



Attach the package and use:
library("DEGRE")
Maintained by
Douglas Terra Machado
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-11-01
Latest Update: 2022-11-02
Description:
Genes that are differentially expressed between two or more experimental conditions can be detected in RNA-Seq. A high biological variability may impact the discovery of these genes once it may be divergent between the fixed effects. However, this variability can be covered by the random effects. 'DEGRE' was designed to identify the differentially expressed genes considering fixed and random effects on individuals. These effects are identified earlier in the experimental design matrix. 'DEGRE' has the implementation of preprocessing procedures to clean the near zero gene reads in the count matrix, normalize by 'RLE' published in the 'DESeq2' package, 'Love et al. (2014)' and it fits a regression for each gene using the Generalized Linear Mixed Model with the negative binomial distribution, followed by a Wald test to assess the regression coefficients.
How to cite:
Douglas Terra Machado (2022). DEGRE: Inferring Differentially Expressed Genes using Generalized Linear Mixed Models. R package version 0.2.0, https://cran.r-project.org/web/packages/DEGRE. Accessed 07 Oct. 2026.
Previous versions and publish date:
0.1.0 (2022-11-01 15:33), 0.2.0 (2022-11-02 10:32), (2026-07-09 08:01)
Other packages that cited DEGRE R package
View DEGRE citation profile
Other R packages that DEGRE depends, imports, suggests or enhances
Complete documentation for DEGRE
Functions, R codes and Examples using the DEGRE R package
Some associated functions: BarGraphDEGRE . DEGRE . DEGRE_package . VolcanoDEGRE . 
Some associated R codes: BarGraphDEGRE.R . DEGRE.R . DEGRE_package.R . VolcanoDEGRE.R .  Full DEGRE package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

ggTimeSeries  
Time Series Visualisations Using the Grammar of Graphics
Provides additional display mediums for time series visualisations. ...
Download / Learn more Package Citations See dependency  
plaqr  
Partially Linear Additive Quantile Regression
Estimation, prediction, thresholding, transformation, and plotting for partially linear additive qua ...
Download / Learn more Package Citations See dependency  
splm  
Econometric Models for Spatial Panel Data
ML and GM estimation and diagnostic testing of econometric models for spatial panel data. ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
blandr  
Bland-Altman Method Comparison
Carries out Bland Altman analyses (also known as a Tukey mean-difference plot) as described by JM B ...
Download / Learn more Package Citations See dependency  
skewlmm  
Scale Mixture of Skew-Normal Linear Mixed Models
It fits scale mixture of skew-normal linear mixed models using an expectation–maximization (EM) ty ...
Download / Learn more Package Citations See dependency  

28,905

R Packages

247,686

Dependencies

76,495

Author Associations

28,906

Publication Badges

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