Man pages for LXQin/DANA
Data-driven Normalization Assessment for miRNA-Seq Data
| applyNormalization | Applies normalization methods to given data set |
| assessNormalization | Data-driven miRNA sequencing Normalization Assessment |
| compute.cc | Compute the concordance correlation of clustered positive... |
| compute.mscr | Compute the mean correlation reduction in negative controls |
| defineClusters | Polycistronic clustering of miRNAs |
| defineControls | Definition of negative and positive control miRNAs for DANA... |
| listClusters | Convert gene-wise clusters into nested list |
| miRNA.coordinates | Chromosomal coordinate for miRNA (hsa) from MiRBase v22 |
| norm.DESeq | DESeq Normalization |
| norm.Med | Median (Med) Normalization |
| norm.PoissonSeq | PoissonSeq Normalization |
| norm.QN | Quantile Normalization (QN) |
| norm.RUV | Normalization By Remove Unwanted Variation (RUV) |
| norm.TC | Total Count (TC) Normalization |
| norm.TMM | Trimmed Mean of M-values (TMM) Normalization |
| norm.UQ | Upper Quartile (UQ) Normalization |
| partialCor | Partial correlation estimation |
| pearsonCor | Pearson correlation estimation |
| plotCor | Correlation plot for partial correlations within... |
| plotCountHist | Read count histogram |
| plotDANA | Scatter plot DANA assessment metrics |
| plotMeanSD | Mean-Standard Deviation Plot |
| prec2corr | Computes partial correlation matrix from a given precision... |
