SVAPLSseq

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last 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>

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

Installation

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


if (!require("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")
SVAPLSseq tutorial PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, GeneExpression, ImmunoOncology, Normalization, RNASeq, Software
Version 1.10.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends R (>= 3.4)
Imports methods, stats, SummarizedExperiment, edgeR, ggplot2, limma, lmtest, parallel, pls
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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
Bioc Package Browser https://code.bioconductor.org/browse/SVAPLSseq/
Package Short Url https://bioconductor.org/packages/SVAPLSseq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive