TREG

DOI: 10.18129/B9.bioc.TREG    

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

Bioconductor version: Release (3.15)

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>

Citation (from within R, enter citation("TREG")):

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 1.0.1
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
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_1.0.1.tar.gz
Windows Binary TREG_1.0.1.zip
macOS Binary (x86_64) TREG_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/TREG
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TREG
Package Short Url https://bioconductor.org/packages/TREG/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.15 Source Archive

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