awst

DOI: 10.18129/B9.bioc.awst    

This is the development version of awst; for the stable release version, see awst.

Asymmetric Within-Sample Transformation

Bioconductor version: Development (3.15)

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")):

Installation

To install this package, start R (version "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.3.0
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_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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

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