Other packages > Find by keyword >

BRETIGEA  

Brain Cell Type Specific Gene Expression Analysis
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("BRETIGEA", "1.0.3")



Attach the package and use:
library("BRETIGEA")
Maintained by
Andrew McKenzie
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-09-30
Latest Update: 2021-05-05
Description:
Analysis of relative cell type proportions in bulk gene expression data. Provides a well-validated set of brain cell type-specific marker genes derived from multiple types of experiments, as described in McKenzie (2018) . For brain tissue data sets, there are marker genes available for astrocytes, endothelial cells, microglia, neurons, oligodendrocytes, and oligodendrocyte precursor cells, derived from each of human, mice, and combination human/mouse data sets. However, if you have access to your own marker genes, the functions can be applied to bulk gene expression data from any tissue. Also implements multiple options for relative cell type proportion estimation using these marker genes, adapting and expanding on approaches from the 'CellCODE' R package described in Chikina (2015) . The number of cell type marker genes used in a given analysis can be increased or decreased based on your preferences and the data set. Finally, provides functions to use the estimates to adjust for variability in the relative proportion of cell types across samples prior to downstream analyses.
How to cite:
Andrew McKenzie (2018). BRETIGEA: Brain Cell Type Specific Gene Expression Analysis. R package version 1.0.3, https://cran.r-project.org/web/packages/BRETIGEA. Accessed 05 Jun. 2026.
Previous versions and publish date:
1.0.0 (2018-09-30 15:50)
Other packages that cited BRETIGEA R package
View BRETIGEA citation profile
Other R packages that BRETIGEA depends, imports, suggests or enhances
Complete documentation for BRETIGEA
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

ibb  
R Wrapper for Istanbul Municipality Open Data Portal
Call wrappers for Istanbul Metropolitan Municipality's Open Data Portal (Turkish: Istanbul B ...
Download / Learn more Package Citations See dependency  
envirem  
Generation of ENVIREM Variables
Generation of bioclimatic rasters that are complementary to the typical 19 bioclim variables. ...
Download / Learn more Package Citations See dependency  
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  
crossurr  
Cross-Fitting for Doubly Robust Evaluation of High-Dimensional Surrogate Markers
Doubly robust methods for evaluating surrogate markers as outlined in: Agniel D, Hejblum BP, Thiebau ...
Download / Learn more Package Citations See dependency  
msm  
Multi-State Markov and Hidden Markov Models in Continuous Time
Functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal d ...
Download / Learn more Package Citations See dependency  

27,268

R Packages

233,548

Dependencies

72,590

Author Associations

27,205

Publication Badges

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