yarn

DOI: 10.18129/B9.bioc.yarn    

This is the development version of yarn; for the stable release version, see yarn.

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

Bioconductor version: Development (3.17)

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 "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("yarn")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	Annotation, Clustering, GeneExpression, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version	1.25.0
In Bioconductor since	BioC 3.4 (R-3.3) (6 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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/yarn
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/yarn
Package Short Url	https://bioconductor.org/packages/yarn/
Package Downloads Report	Download Stats