awst

This is the released version of awst; for the devel version, see awst.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

Asymmetric Within-Sample Transformation

Bioconductor version: Release (3.23)

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] ORCID: 0000-0001-8508-5012 , Stefano Pagnotta [aut, cph] ORCID: 0000-0002-8298-9777

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

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

Davide Risso, Stefano Pagnotta. awst: Asymmetric Within-Sample Transformation. doi:10.18129/B9.bioc.awst, R package version 1.20.0, https://bioconductor.org/packages/awst.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.20.0
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 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

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, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	awst_1.20.0.tar.gz
Windows Binary (x86_64)	awst_1.20.0.zip
macOS Binary (big-sur-x86_64)	awst_1.20.0.tgz
macOS Binary (sonoma-arm64)	awst_1.20.0.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
Old Source Packages for BioC 3.23	Source Archive