qsvaR

DOI: 10.18129/B9.bioc.qsvaR    

Generate Quality Surrogate Variable Analysis for Degradation Correction

Bioconductor version: Release (3.15)

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>

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

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 1.0.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
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_1.0.0.tar.gz
Windows Binary qsvaR_1.0.0.zip
macOS 10.13 (High Sierra) qsvaR_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/qsvaR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/qsvaR
Package Short Url https://bioconductor.org/packages/qsvaR/
Package Downloads Report Download Stats

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