TREG

DOI: 10.18129/B9.bioc.TREG  

Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Bioconductor version: Release (3.16)

RNA abundance and cell size parameters could improve RNA-seq deconvolution algorithms to more accurately estimate cell type proportions given the different cell type transcription activity levels. A Total RNA Expression Gene (TREG) can facilitate estimating total RNA content using single molecule fluorescent in situ hybridization (smFISH). We developed a data-driven approach using a measure of expression invariance to find candidate TREGs in postmortem human brain single nucleus RNA-seq. This R package implements the method for identifying candidate TREGs from snRNA-seq data.

Author: Louise Huuki-Myers [aut, cre] , Leonardo Collado-Torres [ctb]

Maintainer: Louise Huuki-Myers <lahuuki at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TREG")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TREG")

 

HTML	R Script	How to find Total RNA Expression Genes (TREGs)
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	Artistic-2.0
Depends	R (>= 4.2), SummarizedExperiment
Imports	Matrix, purrr, rafalib
LinkingTo
Suggests	BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment
SystemRequirements
Enhances
URL	https://github.com/LieberInstitute/TREG http://research.libd.org/TREG/
BugReports	https://support.bioconductor.org/t/TREG
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	TREG_1.2.0.tar.gz
Windows Binary	TREG_1.2.0.zip
macOS Binary (x86_64)	TREG_1.2.0.tgz
macOS Binary (arm64)	TREG_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TREG
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TREG
Bioc Package Browser	https://code.bioconductor.org/browse/TREG/
Package Short Url	https://bioconductor.org/packages/TREG/
Package Downloads Report	Download Stats