Man pages for Vitek-Lab/MSstatsPTM
Statistical Characterization of Post-translational Modifications
| annotSite | Annotate modification site |
| dataProcessPlotsPTM | Visualization for explanatory data analysis |
| dataSummarizationPTM | Data summarization function for label-free MS experiments... |
| dataSummarizationPTM_TMT | Data summarization function for TMT labelled MS experiments... |
| designSampleSizePTM | Planning future experimental designs of PTM experiments in... |
| DIANNtoMSstatsPTMFormat | Convert the output of DIA-NN PSM file into MSstatsPTM format |
| dot-calculatePowerPTM | Power calculation for PTM experiment |
| dot-fixTerminus | Add site location and aa |
| dot-getNumSamplePTM | Get sample size for PTM experiment |
| dot-joinFasta | Add FASTA data into dataframe |
| dot-locateSites | Add site location and aa |
| dot-removeCutoffSites | Remove sites below cutoff probability |
| fragpipe_annotation | Example annotation file for a TMT FragPipe experiment. |
| fragpipe_annotation_protein | Example annotation file for a global profiling run TMT... |
| fragpipe_input | Output of FragPipe TMT PTM experiment |
| fragpipe_input_protein | Output of FragPipe TMT global profiling experiment |
| FragPipetoMSstatsPTMFormat | Convert output of TMT labeled Fragpipe data into MSstatsPTM... |
| groupComparisonPlotsPTM | Visualization for model-based analysis and summarization |
| groupComparisonPTM | Perform differential analysis on MS-based proteomics... |
| locateMod | Locate modified sites with a peptide |
| locatePTM | Annotate modified sites with associated peptides |
| maxq_lf_annotation | Example annotation file for a label-free MaxQuant experiment. |
| maxq_lf_evidence | Example MaxQuant evidence file from the output of a label... |
| maxq_tmt_annotation | Example annotation file for a TMT MaxQuant experiment. |
| maxq_tmt_evidence | Example MaxQuant evidence file from the output of a TMT... |
| MaxQtoMSstatsPTMFormat | Convert output of label-free or TMT MaxQuant experiments into... |
| MetamorpheusToMSstatsPTMFormat | Import Metamorpheus files into PTM format |
| MSstatsPTM | MSstatsPTM: A package for detecting differentially abundant... |
| MSstatsPTMSiteLocator | Locate modification site number and amino acid |
| pd_annotation | Example annotation file for a label-free Proteome Discoverer... |
| pd_psm_input | Example Proteome Discoverer evidence file from the output of... |
| pd_testing_output | Example output of Proteome Discoverer converter |
| PDtoMSstatsPTMFormat | Convert Proteome Discoverer output into MSstatsPTM format |
| ProgenesistoMSstatsPTMFormat | Converts non-TMT Progenesis output into the format needed for... |
| ProteinProspectortoMSstatsPTMFormat | Generate MSstatsPTM required input format from Protein... |
| PStoMSstatsPTMFormat | Convert Peaks Studio output into MSstatsPTM format |
| raw.input | Example of input PTM dataset for LabelFree/DDA/DIA... |
| raw.input.tmt | Example of input PTM dataset for TMT experiments. |
| SkylinetoMSstatsPTMFormat | Convert Skyline output into MSstatsPTM format |
| spectronaut_annotation | Example annotation file for a label-free Spectronaut... |
| spectronaut_input | Example Spectronaut evidence file from the output of a label... |
| SpectronauttoMSstatsPTMFormat | Convert Spectronaut output into MSstatsPTM format |
| summary.data | Example of output from dataSummarizationPTM function for... |
| summary.data.tmt | Example of output from dataSummarizationPTM_TMT function for... |
| tidyFasta | Read and tidy a FASTA file |
