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

Bioconductor version: Release (3.19)

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))


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 1.8.0
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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Follow Installation instructions to use this package in your R session.

Source Package TREG_1.8.0.tar.gz
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macOS Binary (x86_64) TREG_1.8.0.tgz
macOS Binary (arm64) TREG_1.8.0.tgz
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Source Repository (Developer Access) git clone
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