awst

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

Asymmetric Within-Sample Transformation

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DOI: 10.18129/B9.bioc.awst

Bioconductor version: Development (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 iD ORCID: 0000-0001-8508-5012 , Stefano Pagnotta [aut, cph] ORCID iD ORCID: 0000-0002-8298-9777

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

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

Installation

To install this package, start R (version "4.6") 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.