awst
This is the development version of awst; for the stable release version, see awst.
Asymmetric Within-Sample Transformation
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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_1.21.0.tar.gz |
| Windows Binary (x86_64) | awst_1.21.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | awst_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | awst_1.21.0.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 |