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 22 Dec. 2024.
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
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
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
Rfast2  
A Collection of Efficient and Extremely Fast R Functions II
A collection of fast statistical and utility functions for data analysis. Functions for regression, ...
Download / Learn more Package Citations See dependency  
dmlalg  
Double Machine Learning Algorithms
Implementation of double machine learning (DML) algorithms in R, based on Emmenegger and Buehlmann ...
Download / Learn more Package Citations See dependency  
wordspace  
Distributional Semantic Models in R
An interactive laboratory for research on distributional semantic models ('DSM', see < ...
Download / Learn more Package Citations See dependency  
LOGANTree  
Tree-Based Models for the Analysis of Log Files from Computer-Based Assessments
Enables researchers to model log-file data from computer-based assessments using machine-learning te ...
Download / Learn more Package Citations See dependency  
Maintainer: Qi Qin (view profile)
elect  
Estimation of Life Expectancies Using Multi-State Models
Functions to compute state-specific and marginal life expectancies. The computation is based on a fi ...
Download / Learn more Package Citations See dependency  

23,394

R Packages

201,798

Dependencies

63,416

Author Associations

23,395

Publication Badges

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