DOI: 10.18129/B9.bioc.SVAPLSseq    

This package is for version 3.8 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: 3.8

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>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script SVAPLSseq tutorial
PDF   Reference Manual
Text   NEWS


biocViews BatchEffect, GeneExpression, ImmunoOncology, Normalization, RNASeq, Software
Version 1.8.1
In Bioconductor since BioC 3.4 (R-3.3) (2.5 years)
License GPL-3
Depends R (>= 3.4)
Imports methods, stats, SummarizedExperiment, edgeR, ggplot2, limma, lmtest, parallel, pls
Suggests BiocStyle
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_1.8.1.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) SVAPLSseq_1.8.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: