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
Previous versions and publish date:
0.1.0 (2022-11-01 15:33)
Other packages that cited DEGRE R package
View DEGRE citation profile
Other R packages that DEGRE depends, imports, suggests or enhances
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
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

factorplot  
Graphical Presentation of Simple Contrasts
Methods to calculate, print, summarize and plot pairwise differences from GLMs, GLHT or Multinomial ...
Download / Learn more Package Citations See dependency  
cdcfluview  
Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ("CDC") "FluView" Portal
The 'U.S.' Centers for Disease Control and Prevention (CDC) maintain a portal ...
Download / Learn more Package Citations See dependency  
QuantileNPCI  
Nonparametric Confidence Intervals for Quantiles
Based on Alan D. Hutson (1999) , "Calculating nonparametric confidence i ...
Download / Learn more Package Citations See dependency  
Maintainer: Li Yan (view profile)
r2resize  
In-Text Resizer for Images, Tables and Fancy Resizable 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  
FMCCSD  
Efficient Estimation of Clustered Current Status Data
Current status data abounds in the field of epidemiology and public health, where the only observab ...
Download / Learn more Package Citations See dependency  
srm  
Structural Equation Modeling for the Social Relations Model
Provides functionality for structural equation modeling for the social relations model (Kenny & ...
Download / Learn more Package Citations See dependency  

22,114

R Packages

188,080

Dependencies

55,244

Author Associations

22,115

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net. Contact Us / Suggestions / Concerns