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

## Documentation for package ‘yarn’ version 1.39.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help 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 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