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

Documentation for package ‘yarn’ version 1.6.0

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 and control genes.
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 a given group/tissue
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