analyzeDuprates | Read in a BAM file and count the tags falling on the features described in the GTF file |
bamutilMarkDuplicates | Mark duplicates using bamutil |
cumulativeDuprateBarplot | Barplot showing the cumulative read counts fraction |
dm | Duplication matrix of a good RNASeq experiment |
dm.bad | Duplication matrix of a failed RNASeq experiment |
dupRadar | dupRadar. |
dupRadar_examples | Example data containing precomputed matrices for two RNASeq experiments |
duprateExpBoxplot | Duplication rate ~ total reads per kilobase (RPK) boxplot |
duprateExpDensPlot | Duplication rate ~ total read count plot |
duprateExpFit | Duplication rate ~ total read count fit model |
duprateExpIdentify | Identify genes plotted by 'duprateExpPlot' |
duprateExpPlot | Duplication rate ~ total read count plot |
expressionHist | Draw histogram with the expression values |
getBinDuplication | Helper function used in 'duprateExpBoxplot' |
getBinRpkMean | Helper function used in 'duprateExpBoxplot' |
getDupMatBin | Helper function used in 'getBinDuplication' and 'getBinRpkMean' |
getDupMatStats | Report duplication stats on regions |
getDynamicRange | Dynamic range |
getRpkBinReadCountFraction | Helper function used in 'readcountExpressionBoxplot' |
getRpkCumulativeReadCountFraction | Helper function used in 'readcountExpressionBoxplot' |
markDuplicates | Program dispatchers to mark duplicated reads from a BAM file |
picardMarkDuplicates | Mark duplicates using Picard tools |
readcountExpBoxplot | Barplot of percentage of reads falling into expression bins |