# Tools for quantitative proteomics data analysis

## Documentation for package ‘qPLEXanalyzer’ version 1.28.2

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

## Help Pages

qPLEXanalyzer-package | Tools for qPLEX-RIME data analysis
assignColours | Assigns colours to samples in groups
coefVar | Calculating the coefficient of variation by utilizing expression data within individual sample groups.
computeDiffStats | Compute differential statistics
convertToMSnset | Converts proteomics TMT intensity data to MSnSet
corrPlot | Correlation plot
coveragePlot | Plot peptide sequence coverage
ER_ARID1A_KO_MCF7 | ER_ARID1A_KO_MCF7 dataset
exp2_Xlink | exp2_Xlink dataset
exp3_OHT_ESR1 | exp3_OHT_ESR1 dataset
getContrastResults | Get differential statistics results
groupScaling | Normalization by scaling within group
hierarchicalPlot | Hierarchical clustering plot
human_anno | human_anno dataset
intensityBoxplot | Intensity Distribution boxplot
intensityPlot | Intensity Distribution Plot
IRSnorm | Batch Correction by Internal Reference Scale
maVolPlot | MA or Volcano Plot
mergePeptides | Merge identical modified peptides intensities
mergeSites | Merge identical modification sites intensities
mouse_anno | mouse_anno dataset
normalizeQuantiles | Quantile normalization
normalizeScaling | Normalization by scaling
pcaPlot | PCA plot
peptideIntensityPlot | Plot peptide intensities
plotMeanVar | Mean variance plot
qPLEXanalyzer | Tools for qPLEX-RIME data analysis
regressIntensity | Regression based analysis
rliPlot | Relative log intensity plot
rowScaling | Normalization by scaling peptide/protein intensity across all samples
summarizeIntensities | Summarizes peptides intensities to proteins