Tools for quantitative proteomics data analysis
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Documentation for package ‘qPLEXanalyzer’ version 1.24.0
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 |