qPLEXanalyzer-package: Tools for qPLEX-RIME data analysis

In crukci-bioinformatics/qPLEXanalyzer: Tools for quantitative proteomics data analysis

Tools for qPLEX-RIME data analysis

Description

Tools for quantitiative proteomics data analysis generated from qPLEX-RIME method The package offers the following functionalities Data processing, normalization & analysis:

• convertToMSnset: Converts quantitative data to a MSnSet

• summarizeIntensities: Summarizes multiple peptide measurements for a protein

• normalizeQuantiles: Performs quantile normalization on the peptides/proteins intensities

• normalizeScaling: Performs scaling normalization on the peptides/proteins intensities (mean, median or sum)

• groupScaling: Performs scaling normalization on the peptides/proteins intensities within group (median or mean)

• rowScaling: Normalization by scaling peptide/protein intensity across all samples

• regressIntensity: Performs linear regression on protein intensities based on selected protein

• coefVar: Calculating the coefficient of variation by utilizing expression data within individual sample groups

• computeDiffStats: Compute differential statistics for the given contrasts

• getContrastResults: Get differential statistics results for given contrast

Visualization:

• assignColours: Assigns colours to samples in groups

• corrPlot: Correlation plot of all the samples

• coveragePlot: Computes and display protein sequence coverage of

• hierarchicalPlot: Hierarchical clustering plot of all the samples

• intensityBoxplot: Intensity distribution boxplot of all the samples

• intensityPlot: Intensity distribution plot of all the samples

• maVolPlot: MA or Volcano plot of differential analysis results

• pcaPlot: PCA plot of all the samples

• peptideIntensityPlot: Peptide intensity distribution plot of specific protein

• plotMeanVar: Computes and plots mean-variance for samples in MSnSet

• rliPlot: Relative intensity plot of all the samples selected protein in proteomics experiment

Author(s)

Matthew Eldridge, Kamal Kishore, Ashley Sawle (Maintainer)

[e-mail]

See Also

Useful links:

• Report bugs at https://github.com/crukci-bioinformatics/qPLEXanalyzer/issues

crukci-bioinformatics/qPLEXanalyzer documentation built on June 12, 2025, 7:41 p.m.