MSstats-package |
Tools for protein significance analysis in DDA,SRM and DIA for label-free or label-based proteomic experiments |
dataProcess |
Data pre-processing and quality control of MS runs of raw data |
dataProcessPlots |
Visualization for explanatory data analysis |
designSampleSize |
Planning future experimental designs of label-free and label-based LC-MS, SRM, DIA experiments in sample size calculation |
designSampleSizePlots |
Visualization for sample size calculation |
groupComparison |
Finding differentially abundant proteins across conditions in LC-MS, SRM and DIA experiment |
groupComparisonPlots |
Visualization for model-based analysis and summarizing differentially abundant proteins |
modelBasedQCPlots |
Visualization for model-based quality control in fitting model |
MSstats |
Tools for protein significance analysis in DDA,SRM and DIA for label-free or label-based proteomic experiments |
QuantData |
Quantitative data after data pre-processing and quality control of MS runs |
quantification |
Protein sample quantification or group quantification |
RawData |
Example dataset from a label-based SRM experiment of a time course yeast study |
testResultMultiComparisons |
Significance testing result of a set of comparisons between two groups |
testResultOneComparison |
Significance testing result of one comparison between two groups |
transformMSnSetToMSstats |
Transforms a MSnSet class dataset into a required input for MSstats |
transformMSstatsToMSnSet |
Transformation input format for MSstats to MSnSet class |