TREG
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
Bioconductor version: 3.23 · Package version: 1.16.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TREG")Details
| Maintainer | Louise Huuki-Myers <lahuuki@gmail.com> |
| Author | Louise Huuki-Myers [aut, cre] (ORCID: <https://orcid.org/0000-0001-5148-3602>), Leonardo Collado-Torres [ctb] (ORCID: <https://orcid.org/0000-0003-2140-308X>) |
| License | Artistic-2.0 |
| URL | https://github.com/LieberInstitute/TREG, http://research.libd.org/TREG/ |
| Bug Reports | https://support.bioconductor.org/t/TREG |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/TREG/ |
Citation
From within R, enter citation("TREG"):
Louise Huuki-Myers. TREG: Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data. doi:10.18129/B9.bioc.TREG, R package version 1.16.0, https://bioconductor.org/packages/TREG.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the 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 (arm64) | TREG_1.16.0.tgz |
| macOS binary (x86_64) | TREG_1.16.0.tgz |
Dependencies
Depends: R (>= 4.2), SummarizedExperiment
Imports: Matrix, purrr, rafalib
Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment