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

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Documentation for package ‘dropestr’ version 0.7.9

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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.