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>

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")

# 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

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