annotSite()
|
Annotate modification site |
dataProcessPlotsPTM()
|
Visualization for explanatory data analysis |
dataSummarizationPTM()
|
Process MS PTM and global protein data |
dataSummarizationPTM_TMT()
|
Process MS PTM and global protein data produced via tandem mass tag labeling |
globalConverterPTM()
|
General converter function for MSstatsPTM. |
groupComparisonPlotsPTM()
|
Visualization for model-based analysis and summarization |
groupComparisonPTM()
|
Model PTM and/or protein data and make adjustments if needed |
locateMod()
|
Locate modified sites with a peptide |
locatePTM()
|
Annotate modified sites with associated peptides |
MaxQtoMSstatsPTMFormat()
|
Convert output of TMT labeled MaxQuant experiment into MSstatsPTM format |
MSstatsPTM
|
MSstatsPTM: A package for detecting differencially abundant post
translational modifications (PTM) in shotgun mass spectrometry-bsed proteomic
experiments. |
ProgenesistoMSstatsPTMFormat()
|
Converts non-TMT Progenesis output into the format needed for MSstatsPTM |
raw.input
|
Example of input PTM dataset for LabelFree/DDA/DIA experiments. |
raw.input.tmt
|
Example of input PTM dataset for TMT experiments. |
tidyFasta()
|
Read and tidy a FASTA file |