# Preprocessing of Droplet-based Single-Cell RNA-seq Data

## Documentation for package ‘dropestr’ version 0.7.9

- DESCRIPTION file.

## Help Pages

ArrayDerivative | Calculate derivative of an tabular function.
Center | Center numeric data.
EstimateCellsNumber | Get the coordinates of the longest true seqeunce of a logical vector.
EstimateSaturation | Estimate library saturation with preseqR
FillAdjacentUmisData | Fill information about adjacent UMIs, their probabilities and differences for each UMI.
FractionSmoothScatter | Plot smoothScatter of geneset fraction for each cell by cell rank
GetLongestTrue | Get the coordinates of the longest true seqeunce of a logical vector.
GetOptimalPcs | Perform PCA with the optimal number of principal components.
GetUmisDistribution | Estimate a distribution of observed UMI probabilities.
hello | Hello, World!
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 cells.
PlotCellsNumberLine | Plot for the estimation of the number 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.
PrepareLqCellsDataPipeline | Prepare data frame for low-quality cells filtration.
reads_per_umi_per_cell | Results of processing of 10x Frozen Human PBMC (Donor A) dataset, neccesary for UMI errors correction. 50 largest cells. https://support.10xgenomics.com/single-cell-gene-expression/datasets/1.1.0/frozen_pbmc_donor_a
saturation_srr1784312 | Results of saturation analysis of SRR1784312 dataset (mouse ES cells).
Scale | Center and normalized numeric data.
ScoreCells | Score cells with a KDE classifier.
ScorePipelineCells | Score cells with a KDE classifier.
TrainKDE | Train binary KDE classifier.