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("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 | R Script | |
| Reference Manual | ||
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 |