SVAPLSseq

DOI: 10.18129/B9.bioc.SVAPLSseq    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SVAPLSseq.

SVAPLSseq-An R package to estimate the hidden factors of unwanted variability and adjust for them to enable a more powerful and accurate differential expression analysis based on RNAseq data

Bioconductor version: 3.9

The package contains functions that are intended for extracting the signatures of latent variation in RNAseq data and using them to perform an improved differential expression analysis for a set of features (genes, transcripts) between two specified biological groups.

Author: Sutirtha Chakraborty

Maintainer: Sutirtha Chakraborty <sutirtha_sutir at yahoo.co.in>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SVAPLSseq")

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("SVAPLSseq")

 

PDF	R Script	SVAPLSseq tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, GeneExpression, ImmunoOncology, Normalization, RNASeq, Software
Version	1.10.0
In Bioconductor since	BioC 3.4 (R-3.3) (3 years)
License	GPL-3
Depends	R (>= 3.4)
Imports	methods, stats, SummarizedExperiment, edgeR, ggplot2, limma, lmtest, parallel, pls
LinkingTo
Suggests	BiocStyle
SystemRequirements
Enhances
URL
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	SVAPLSseq_1.10.0.tar.gz
Windows Binary	SVAPLSseq_1.10.0.zip
Mac OS X 10.11 (El Capitan)	SVAPLSseq_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SVAPLSseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SVAPLSseq
Package Short Url	https://bioconductor.org/packages/SVAPLSseq/
Package Downloads Report	Download Stats