TREG
This is thereleased version of TREG; for the devel version, seeTREG.
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0001-5148-3602, Leonardo Collado-Torres [ctb] ORCID: 0000-0003-2140-308X
Maintainer: Louise Huuki-Myers <lahuuki at gmail.com>
citation("TREG")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("TREG")For older versions of R, please refer to the appropriateBioconductor 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 | 1.14.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2),SummarizedExperiment |
| Imports | Matrix,purrr,rafalib |
| System Requirements | |
| URL | https://github.com/LieberInstitute/TREGhttp://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 |
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| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | TREG_1.14.0.tar.gz |
| Windows Binary (x86_64) | TREG_1.14.0.zip |
| macOS Binary (x86_64) | TREG_1.14.0.tgz |
| macOS Binary (arm64) | TREG_1.14.0.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 |