yarn
This is the released version of yarn; for the devel version, see yarn.
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
Bioconductor version: Release (3.23)
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("yarn")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Clustering, GeneExpression, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization |
| Version | 1.38.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 years) |
| License | Artistic-2.0 |
| Depends | Biobase |
| Imports | biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat (>= 0.8) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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_1.38.0.tar.gz |
| Windows Binary (x86_64) | yarn_1.38.0.zip |
| macOS Binary (big-sur-x86_64) | yarn_1.38.0.tgz |
| macOS Binary (sonoma-arm64) | yarn_1.38.0.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 |