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qsvaR

Generate Quality Surrogate Variable Analysis for Degradation Correction


Bioconductor version: Release (3.18)

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.

Author: Joshua Stolz [aut] , Hedia Tnani [ctb, cre] , Leonardo Collado-Torres [ctb]

Maintainer: Hedia Tnani <hediatnani0 at gmail.com>

Citation (from within R, enter citation("qsvaR")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("qsvaR")

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("qsvaR")
Introduction to qsvaR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiologicalQuestion, Coverage, DifferentialExpression, Normalization, Sequencing, Software, WorkflowStep
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License Artistic-2.0
Depends R (>= 4.2), SummarizedExperiment
Imports sva, stats, ggplot2, methods
System Requirements
URL https://github.com/LieberInstitute/qsvaR
Bug Reports https://support.bioconductor.org/t/qsvaR
See More
Suggests BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package qsvaR_1.6.0.tar.gz
Windows Binary qsvaR_1.6.0.zip
macOS Binary (x86_64) qsvaR_1.6.0.tgz
macOS Binary (arm64) qsvaR_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/qsvaR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/qsvaR
Bioc Package Browser https://code.bioconductor.org/browse/qsvaR/
Package Short Url https://bioconductor.org/packages/qsvaR/
Package Downloads Report Download Stats