qsvaR
Generate Quality Surrogate Variable Analysis for Degradation Correction
Bioconductor version: 3.24 · Package version: 1.17.0
The qsvaR package contains functions for removing the effect of degration in rna-seq data from postmortem brain tissue. The package is equipped to help users generate principal components associated with degradation. The components can be used in differential expression analysis to remove the effects of degradation.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("qsvaR")Details
| Maintainer | Nicholas J. Eagles <nickeagles77@gmail.com> |
| Author | Joshua Stolz [aut] (ORCID: <https://orcid.org/0000-0001-5694-5247>), Hedia Tnani [ctb] (ORCID: <https://orcid.org/0000-0002-0380-9740>), Leonardo Collado-Torres [ctb] (ORCID: <https://orcid.org/0000-0003-2140-308X>), Nicholas J. Eagles [aut, cre] (ORCID: <https://orcid.org/0000-0002-9808-5254>) |
| License | Artistic-2.0 |
| URL | https://github.com/LieberInstitute/qsvaR |
| Bug Reports | https://support.bioconductor.org/t/qsvaR |
| Downloads rank | 404 |
| Source branch | devel |
| biocViews | BiologicalQuestion, Coverage, DifferentialExpression, Normalization, Sequencing, Software, WorkflowStep |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | qsvaR_1.17.0.tar.gz |
| Windows binary (x86_64) | qsvaR_1.17.0.zip |
| macOS binary (arm64) | qsvaR_1.17.0.tgz |
| macOS binary (x86_64) | qsvaR_1.17.0.tgz |
Dependencies
Depends: R (>= 4.2), SummarizedExperiment
Imports: dplyr, sva, stats, ggplot2, rlang, methods
Suggests: BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0)