qsvaR

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see qsvaR.

Generate Quality Surrogate Variable Analysis for Degradation Correction

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0001-5694-5247 , Hedia Tnani [ctb, cre] ORCID iD ORCID: 0000-0002-0380-9740 , Leonardo Collado-Torres [ctb] ORCID iD ORCID: 0000-0003-2140-308X , Nicholas J. Eagles [aut] ORCID iD ORCID: 0000-0002-9808-5254

Maintainer: Hedia Tnani <hediatnani0 at gmail.com>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BiologicalQuestion, Coverage, DifferentialExpression, Normalization, Sequencing, Software, WorkflowStep

Version 1.12.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 years)

License Artistic-2.0

Depends R (>= 4.2), SummarizedExperiment

Imports dplyr, sva, stats, ggplot2, rlang, methods

System Requirements

URL https://github.com/LieberInstitute/qsvaR

Bug Reports https://support.bioconductor.org/t/qsvaR

Suggests BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0)

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Package Archives

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

Source Package qsvaR_1.12.0.tar.gz

Windows Binary (x86_64) qsvaR_1.12.0.zip (64-bit only)

macOS Binary (x86_64) qsvaR_1.12.0.tgz

macOS Binary (arm64) qsvaR_1.12.0.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/

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