awst

DOI: 10.18129/B9.bioc.awst    

Asymmetric Within-Sample Transformation

Bioconductor version: Release (3.13)

We propose an Asymmetric Within-Sample Transformation (AWST) to regularize RNA-seq read counts and reduce the effect of noise on the classification of samples. AWST comprises two main steps: standardization and smoothing. These steps transform gene expression data to reduce the noise of the lowly expressed features, which suffer from background effects and low signal-to-noise ratio, and the influence of the highly expressed features, which may be the result of amplification bias and other experimental artifacts.

Author: Davide Risso [aut, cre, cph] , Stefano Pagnotta [aut, cph]

Maintainer: Davide Risso <risso.davide at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("awst")

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("awst")

 

HTML	R Script	Introduction to awst
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	MIT + file LICENSE
Depends
Imports	stats, methods, SummarizedExperiment
LinkingTo
Suggests	airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/drisso/awst
BugReports	https://github.com/drisso/awst/issues
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	awst_1.0.0.tar.gz
Windows Binary	awst_1.0.0.zip
macOS 10.13 (High Sierra)	awst_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/awst
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/awst
Package Short Url	https://bioconductor.org/packages/awst/
Package Downloads Report	Download Stats