This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

qsvaR

This is the development version of qsvaR; for the stable release version, see qsvaR.

Generate Quality Surrogate Variable Analysis for Degradation Correction

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.5.3
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2), SummarizedExperiment
Imports sva, stats, ggplot2, methods
Linking To
Suggests BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0)
System Requirements
Enhances
URL https://github.com/LieberInstitute/qsvaR
Bug Reports https://support.bioconductor.org/t/qsvaR
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package qsvaR_1.5.3.tar.gz
Windows Binary qsvaR_1.5.3.zip
macOS Binary (x86_64) qsvaR_1.5.3.tgz
macOS Binary (arm64) qsvaR_1.5.3.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