awst
Asymmetric Within-Sample Transformation
Bioconductor version: Release (3.20)
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("awst")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
Version | 1.14.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
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_1.14.0.tar.gz |
Windows Binary (x86_64) | awst_1.14.0.zip (64-bit only) |
macOS Binary (x86_64) | awst_1.14.0.tgz |
macOS Binary (arm64) | awst_1.13.0.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/ |
Package Downloads Report | Download Stats |