Shiny-based interactive data-quality exploration for omics data

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Documentation for package ‘MatrixQCvis’ version 1.12.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

barplotSamplesMeasuredMissing	Barplot of number of measured/missing features of samples
batchCorrectionAssay	Remove batch effects from (count/intensity) values of a 'SummarizedExperiment'
createBoxplot	Create a boxplot of (count/intensity) values per sample
createDfFeature	Create data frame of (count/intensity) values for a selected feature along data processing steps
cv	Calculate coefficient of variation
cvFeaturePlot	Plot of feature-wise coefficient of variation values
dimensionReduction	Dimensionality reduction with dimensionReduction methods PCA, PCoA, NMDS, UMAP and tSNE
dimensionReductionPlot	Plot the coordinates from 'dimensionReduction' values
distSample	Create a heatmap using distance information between samples
distShiny	Create distance matrix from numerical matrix
driftPlot	Plot the trend line for aggregated values
ECDF	Create ECDF plot of a sample against a reference
explVar	Retrieve the explained variance for each principal component (PCA) or axis (PCoA)
extractComb	Obtain the features that are present in a specified set
featurePlot	Create a plot of (count/intensity) values over the samples
histFeature	Histogram for measured value per feature
histFeatureCategory	Histogram of features per sample type
hist_sample	Plot a histogram of the number of a category
hist_sample_num	Return the number of a category
hoeffDPlot	Create a plot from a list of Hoeffding's D values
hoeffDValues	Create values of Hoeffding's D statistics from M and A values
imputeAssay	Impute missing values in a 'matrix'
MAplot	Create a MA plot
MAvalues	Create values (M and A) for MA plot
measuredCategory	Obtain the number of measured intensities per sample type
mosaic	Mosaic plot for two factors in colData(se)
normalizeAssay	Normalize a data sets (reduce technical sample effects)
permuteExplVar	Permute the expression values and retrieve the explained variance
plotCV	Plot CV values
plotPCALoadings	Plot for PCA loadings of features
plotPCAVar	Plot of explained variance against the principal components
plotPCAVarPvalue	Plot p-values for the significance of principal components
samplesMeasuredMissing	Create tibble containing number of measured/missing features of samples
shinyQC	Shiny application for initial QC exploration of -omics data sets
sumDistSample	Plot the sum of distances to other samples
tblPCALoadings	Return tibble with PCA loadings for features
transformAssay	Transform the (count/intensity) values of a 'data.frame', 'tbl' or 'matrix'
upsetCategory	UpSet plot to display measures values across sample types
volcanoPlot	Volcano plot of fold changes/differences against p-values