yarn

DOI: 10.18129/B9.bioc.yarn    

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

Bioconductor version: Release (3.6)

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 <jpaulson at jimmy.harvard.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("yarn")

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	1.4.0
In Bioconductor since	BioC 3.4 (R-3.3) (1.5 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
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	yarn_1.4.0.tar.gz
Windows Binary	yarn_1.4.0.zip
Mac OS X 10.11 (El Capitan)	yarn_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/yarn
Package Short Url	http://bioconductor.org/packages/yarn/
Package Downloads Report	Download Stats