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

Today's Hot Picks in Authors and Packages

RcppHNSW  
'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors
'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This package provides a minimal R int ...
Download / Learn more Package Citations See dependency  
crossrun  
Joint Distribution of Number of Crossings and Longest Run
Joint distribution of number of crossings and the longest run in a series of independent Bernoulli ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize 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  
deductive  
Data Correction and Imputation Using Deductive Methods
Attempt to repair inconsistencies and missing values in data records by using information from vali ...
Download / Learn more Package Citations See dependency  
kgschart  
KGS Rank Graph Parser
Restore underlining numeric data from rating history graph of KGS (an online platform of the game o ...
Download / Learn more Package Citations See dependency  
pkgdepends  
Package Dependency Resolution and Downloads
Find recursive dependencies of 'R' packages from various sources. Solve the dependencies to obtain ...
Download / Learn more Package Citations See dependency  

23,229

R Packages

199,929

Dependencies

62,984

Author Associations

23,230

Publication Badges

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