yarn

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

Bioconductor version: Release (3.20)

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Clustering, GeneExpression, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version	1.32.0
In Bioconductor since	BioC 3.4 (R-3.3) (8 years)
License	Artistic-2.0
Depends	Biobase
Imports	biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro
System Requirements
URL

Suggests	knitr, rmarkdown, testthat (>= 0.8)
Linking To
Enhances
Depends On Me	netZooR
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	yarn_1.32.0.tar.gz
Windows Binary (x86_64)	yarn_1.32.0.zip
macOS Binary (x86_64)	yarn_1.32.0.tgz
macOS Binary (arm64)	yarn_1.31.0.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