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 (3.21)

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: ), Hedia Tnani [ctb, cre] (ORCID: ), Leonardo Collado-Torres [ctb] (ORCID: )

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")

# 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiologicalQuestion, Coverage, DifferentialExpression, Normalization, Sequencing, Software, WorkflowStep
Version	1.11.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	Artistic-2.0
Depends	R (>= 4.2), SummarizedExperiment
Imports	sva, stats, ggplot2, rlang, tidyverse, 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)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	qsvaR_1.11.0.tar.gz
Windows Binary (x86_64)	qsvaR_1.11.0.zip (64-bit only)
macOS Binary (x86_64)	qsvaR_1.11.0.tgz
macOS Binary (arm64)
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