Man pages for kharchenkolab/dropestr
Preprocessing of Droplet-Based Single-Cell RNA-Seq Data
| ArrayDerivative | Calculate derivative of an tabular function |
| Center | Center numeric data |
| EstimateCellsNumber | Get the coordinates of the longest true seqeunce of a logical... |
| EstimateSaturation | Estimate library saturation with preseqR |
| FillAdjacentUmisData | Fill information about adjacent UMIs, their probabilities and... |
| FractionSmoothScatter | Plot smoothScatter of geneset fraction for each cell by cell... |
| GetLongestTrue | Get the coordinates of the longest true seqeunce of a logical... |
| GetOptimalPcs | Perform PCA with the optimal number of principal components. |
| GetUmisDistribution | Estimate a distribution of observed UMI probabilities. |
| lq_cells_data | Low-quality cells |
| Normalize | Normalize numeric data |
| PlotCellScores | Plot smoothScatter with cell quality scores by cell rank |
| PlotCellsNumberHist | Plot for the estimation of minimal size of high-quality... |
| PlotCellsNumberLine | Plot for the estimation of the number of high-quality cells |
| PlotCellsNumberLogLog | Plot for the estimation of minimal size of high-quality cells... |
| PlotCellsNumberSummary | Plot for the summary of cell numbers (Deprecated). |
| PlotGenesPerCell | Plot distribution of log number of genes by cells |
| PlotIntergenicFractionByChromosomes | Plot fraction of different read types for each chromosome |
| PlotReadsPerUmiByCells | Plot mean number of reads per UMI for each cell by cell rank |
| PlotSaturationEstimates | Plot estimated library saturation |
| PlotUmisDistribution | Plot distribution of UMI |
| PredictKDE | Predict data with the KDE classifier |
| PrepareCellsNumberPlot | Prepare data for plotting the number of cells |
| PrepareLqCellsData | Prepare data.frame for low-quality cells filtration. The more... |
| reads_per_umi_per_cell | Results of processing of 10x Frozen Human PBMC (Donor A)... |
| saturation_srr1784312 | Results of saturation analysis of SRR1784312 dataset (mouse... |
| Scale | Center and normalize numeric data |
| ScoreCells | Score cells with a KDE classifier |
| ScorePipelineCells | Score cells with a KDE classifier. |
| TrainClassifier | Train classifier with TrainKDE |
| TrainKDE | Train binary KDE classifier |
