qsvaR

DOI: 10.18129/B9.bioc.qsvaR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see qsvaR.

Generate Quality Surrogate Variable Analysis for Degradation Correction

Bioconductor version: 3.16

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, cre] , Leonardo Collado-Torres [ctb]

Maintainer: Joshua Stolz <josh.stolz at libd.org>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Introduction to qsvaR
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiologicalQuestion, Coverage, DifferentialExpression, Normalization, Sequencing, Software, WorkflowStep
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	Artistic-2.0
Depends	R (>= 4.2), SummarizedExperiment
Imports	sva, stats, ggplot2, methods
LinkingTo
Suggests	BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/LieberInstitute/qsvaR
BugReports	https://support.bioconductor.org/t/qsvaR
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_1.2.0.tar.gz
Windows Binary	qsvaR_1.2.0.zip
macOS Binary (x86_64)	qsvaR_1.2.0.tgz
macOS Binary (arm64)	qsvaR_1.2.0.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