yarn

DOI: 10.18129/B9.bioc.yarn  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Annotation, Clustering, GeneExpression, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version	1.24.0
In Bioconductor since	BioC 3.4 (R-3.3) (6.5 years)
License	Artistic-2.0
Depends	Biobase
Imports	biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro
LinkingTo
Suggests	knitr, rmarkdown, testthat (>= 0.8)
SystemRequirements
Enhances
URL
Depends On Me	netZooR
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	yarn_1.24.0.tar.gz
Windows Binary	yarn_1.24.0.zip
macOS Binary (x86_64)	yarn_1.24.0.tgz
macOS Binary (arm64)	yarn_1.24.0.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