yarn: YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
Version 1.2.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorJoseph 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]
Bioconductor views Annotation Clustering GeneExpression Normalization Preprocessing QualityControl Sequencing Software Visualization
Date of publicationNone
MaintainerJoseph N Paulson <jpaulson@jimmy.harvard.edu>
LicenseArtistic-2.0
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("yarn")

Man pages

annotateFromBiomart: Annotate your Expression Set with biomaRt
bladder: Bladder RNA-seq data from the GTEx consortium
checkMisAnnotation: Check for wrong annotation of a sample using classical MDS...
checkTissuesToMerge: Check tissues to merge based on gene expression profile
downloadGTEx: Download GTEx files and turn them into ExpressionSet object
extractMatrix: Extract the appropriate matrix
filterGenes: Filter specific genes
filterLowGenes: Filter genes that have less than a minimum threshold CPM for...
filterMissingGenes: Filter genes not expressed in any sample
filterSamples: Filter samples
normalizeTissueAware: Normalize in a tissue aware context
plotCMDS: Plot classical MDS of dataset
plotDensity: Density plots of columns in a matrix
plotHeatmap: Plot heatmap of most variable genes
qsmooth: Quantile shrinkage normalization
qstats: Compute quantile statistics
skin: Skin RNA-seq data from the GTEx consortium

Functions

annotateFromBiomart Man page Source code
bladder Man page
checkMisAnnotation Man page Source code
checkTissuesToMerge Man page Source code
downloadGTEx Man page Source code
extractMatrix Man page Source code
filterGenes Man page Source code
filterLowGenes Man page Source code
filterMissingGenes Man page Source code
filterSamples Man page Source code
normalizeTissueAware Man page Source code
plotCMDS Man page Source code
plotDensity Man page Source code
plotHeatmap Man page Source code
qsmooth Man page Source code
qstats Man page Source code
skin Man page

Files

DESCRIPTION
NAMESPACE
R
R/annotateFromBiomart.R
R/bladder-data.R
R/checkMisAnnotation.R
R/checkTissuesToMerge.R
R/downloadGTEx.R
R/extractMatrix.R
R/filterGenes.R
R/filterLowGenes.R
R/filterMissingGenes.R
R/filterSamples.R
R/normalizeTissueAware.R
R/plotCMDS.R
R/plotDensity.R
R/plotHeatmap.R
R/qsmooth.R
R/qstats.R
R/skin-data.R
README.md
build
build/vignette.rds
data
data/bladder.rdata
data/datalist
data/skin.rdata
inst
inst/NEWS
inst/doc
inst/doc/yarn.R
inst/doc/yarn.Rmd
inst/doc/yarn.pdf
man
man/annotateFromBiomart.Rd
man/bladder.Rd
man/checkMisAnnotation.Rd
man/checkTissuesToMerge.Rd
man/downloadGTEx.Rd
man/extractMatrix.Rd
man/filterGenes.Rd
man/filterLowGenes.Rd
man/filterMissingGenes.Rd
man/filterSamples.Rd
man/normalizeTissueAware.Rd
man/plotCMDS.Rd
man/plotDensity.Rd
man/plotHeatmap.Rd
man/qsmooth.Rd
man/qstats.Rd
man/skin.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test-functions.R
vignettes
vignettes/yarn.Rmd
yarn documentation built on May 20, 2017, 10:54 p.m.