TREG
This is the released version of TREG; for the devel version, see TREG.
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2), SummarizedExperiment |
| Imports | Matrix, purrr, rafalib |
| System Requirements | |
| URL | https://github.com/LieberInstitute/TREG http://research.libd.org/TREG/ |
| Bug Reports | https://support.bioconductor.org/t/TREG |
See More
| Suggests | BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TREG_1.16.0.tar.gz |
| Windows Binary (x86_64) | TREG_1.16.0.zip |
| macOS Binary (big-sur-x86_64) | TREG_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | TREG_1.16.0.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 |