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This is the development version of TREG; for the stable release version, see TREG.

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

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


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

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


biocViews GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics
Version 1.9.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License Artistic-2.0
Depends R (>= 4.2), SummarizedExperiment
Imports Matrix, purrr, rafalib
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Suggests BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment
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Source Package TREG_1.9.0.tar.gz
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