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Asymmetric Within-Sample Transformation

Bioconductor version: Release (3.18)

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>

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


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


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Introduction to awst HTML R Script
Reference Manual PDF


biocViews GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Imports stats, methods, SummarizedExperiment
System Requirements
URL https://github.com/drisso/awst
Bug Reports https://github.com/drisso/awst/issues
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Suggests airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown
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Follow Installation instructions to use this package in your R session.

Source Package awst_1.10.0.tar.gz
Windows Binary awst_1.10.0.zip
macOS Binary (x86_64) awst_1.10.0.tgz
macOS Binary (arm64) awst_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/awst
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/awst
Bioc Package Browser https://code.bioconductor.org/browse/awst/
Package Short Url https://bioconductor.org/packages/awst/
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