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yarn

YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization


Bioconductor version: Release (3.18)

Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.

Author: Joseph N Paulson [aut, cre], Cho-Yi Chen [aut], Camila Lopes-Ramos [aut], Marieke Kuijjer [aut], John Platig [aut], Abhijeet Sonawane [aut], Maud Fagny [aut], Kimberly Glass [aut], John Quackenbush [aut]

Maintainer: Joseph N Paulson <paulson.joseph at gene.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("yarn")

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("yarn")
YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, Clustering, GeneExpression, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License Artistic-2.0
Depends Biobase
Imports biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro
System Requirements
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Suggests knitr, rmarkdown, testthat (>= 0.8)
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Depends On Me netZooR
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package yarn_1.28.0.tar.gz
Windows Binary yarn_1.28.0.zip
macOS Binary (x86_64) yarn_1.28.0.tgz
macOS Binary (arm64) yarn_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/yarn
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/yarn
Bioc Package Browser https://code.bioconductor.org/browse/yarn/
Package Short Url https://bioconductor.org/packages/yarn/
Package Downloads Report Download Stats