Package: awst 1.21.0

Davide Risso

awst: Asymmetric Within-Sample Transformation

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.

Authors:Davide Risso [aut, cre, cph], Stefano Pagnotta [aut, cph]

awst_1.21.0.tar.gz
awst_1.21.0.zip(r-4.7)awst_1.21.0.zip(r-4.6)awst_1.21.0.zip(r-4.5)
awst_1.21.0.tgz(r-4.6-any)awst_1.21.0.tgz(r-4.5-any)
awst_1.21.0.tar.gz(r-4.7-any)awst_1.21.0.tar.gz(r-4.6-any)
awst_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
awst/json (API)
NEWS

# Install 'awst' in R:
install.packages('awst', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/drisso/awst/issues

On BioConductor:awst-1.21.0(bioc 3.24)awst-1.20.0(bioc 3.23)

normalizationgeneexpressionrnaseqsoftwaretranscriptomicssequencingsinglecell

4.95 score 3 stars 15 scripts 403 downloads 2 exports 17 dependencies

Last updated from:c693f86290. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE189
linux-devel-x86_64NOTE300
source / vignettesOK290
linux-release-x86_64NOTE296
macos-release-arm64NOTE198
macos-oldrel-arm64NOTE170
windows-develNOTE236
windows-releaseNOTE210
windows-oldrelNOTE211
wasm-releaseOK170

Exports:awstgene_filter

Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

Introduction to awst

Davide Risso

Rendered fromawst_intro.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2021-05-04
Started: 2021-04-14

Readme and manuals

Help Manual

Help pageTopics
Asymmetric Within-Sample Transformationawst awst,matrix-method awst,SummarizedExperiment-method
Gene filtering based on heterogeneitygene_filter gene_filter,matrix-method gene_filter,SummarizedExperiment-method