Man pages for QuackenbushLab/yarn
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

annotateFromBiomartAnnotate your Expression Set with biomaRt
bladderBladder RNA-seq data from the GTEx consortium
checkMisAnnotationCheck for wrong annotation of a sample using classical MDS...
checkTissuesToMergeCheck tissues to merge based on gene expression profile
downloadGTExDownload GTEx files and turn them into ExpressionSet object
extractMatrixExtract the appropriate matrix
filterGenesFilter specific genes
filterLowGenesFilter genes that have less than a minimum threshold CPM for...
filterMissingGenesFilter genes not expressed in any sample
filterSamplesFilter samples
normalizeTissueAwareNormalize in a tissue aware context
plotCMDSPlot classical MDS of dataset
plotDensityDensity plots of columns in a matrix
plotHeatmapPlot heatmap of most variable genes
qsmoothQuantile shrinkage normalization
qstatsCompute quantile statistics
skinSkin RNA-seq data from the GTEx consortium
QuackenbushLab/yarn documentation built on May 9, 2017, 8:42 p.m.