Welcome to the new bioconductor.org!

awst

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

Asymmetric Within-Sample Transformation


Bioconductor version: Development (3.19)

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 "4.4") and enter:


if (!require("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")
Introduction to awst HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.11.1
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends
Imports stats, methods, SummarizedExperiment
System Requirements
URL https://github.com/drisso/awst
Bug Reports https://github.com/drisso/awst/issues
See More
Suggests airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown
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 awst_1.11.1.tar.gz
Windows Binary awst_1.11.1.zip (64-bit only)
macOS Binary (x86_64) awst_1.11.1.tgz
macOS Binary (arm64) awst_1.11.1.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/
Package Downloads Report Download Stats