qsvaR
This is thereleased version of qsvaR; for the devel version, seeqsvaR.
Generate Quality Surrogate Variable Analysis for Degradation Correction
Bioconductor version: Release (3.22)
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: 0000-0001-5694-5247, Hedia Tnani [ctb] ORCID: 0000-0002-0380-9740, Leonardo Collado-Torres [ctb] ORCID: 0000-0003-2140-308X, Nicholas J. Eagles [aut, cre] ORCID: 0000-0002-9808-5254
Maintainer: Nicholas J. Eagles <nickeagles77 at gmail.com>
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 appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion,Coverage,DifferentialExpression,Normalization,Sequencing,Software,WorkflowStep |
| Version | 1.14.0 |
| 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 |
See More
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | qsvaR_1.14.0.tar.gz |
| Windows Binary (x86_64) | qsvaR_1.14.0.zip (64-bit only) |
| macOS Binary (x86_64) | qsvaR_1.14.0.tgz |
| macOS Binary (arm64) | qsvaR_1.14.0.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 |