awst
This is the development version of awst; for the stable release version, see awst.
Asymmetric Within-Sample Transformation
Bioconductor version: Development (3.21)
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:
Maintainer: Davide Risso <risso.davide at gmail.com>
citation("awst")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.15.0 |
| 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_1.15.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |