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| dupRadar-package | dupRadar. |
| 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 |