TREG
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
Bioconductor version: Release (3.17)
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("TREG")):
Installation
To install this package, start R (version "4.3") 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")| How to find Total RNA Expression Genes (TREGs) | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (1.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2), SummarizedExperiment |
| Imports | Matrix, purrr, rafalib |
| Linking To | |
| Suggests | BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment |
| System Requirements | |
| Enhances | |
| URL | https://github.com/LieberInstitute/TREG http://research.libd.org/TREG/ |
| Bug Reports | https://support.bioconductor.org/t/TREG |
See More
| 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_1.4.0.tar.gz |
| Windows Binary | TREG_1.4.0.zip (64-bit only) |
| macOS Binary (x86_64) | TREG_1.4.0.tgz |
| macOS Binary (arm64) | TREG_1.4.0.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 |