SVAPLSseq

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 yahoo.co.in>

Installation

To install this package, start R (version "3.5") 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	1.8.1
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
LinkingTo
Suggests	BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
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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	SVAPLSseq_1.8.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	SVAPLSseq_1.8.1.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	http://bioconductor.org/packages/SVAPLSseq/
Package Downloads Report	Download Stats