Man pages for Vitek-Lab/MSstatsPTM
Statistical Characterization of Post-translational Modifications

annotSiteAnnotate modification site
dataProcessPlotsPTMVisualization for explanatory data analysis
dataSummarizationPTMData summarization function for label-free MS experiments...
dataSummarizationPTM_TMTData summarization function for TMT labelled MS experiments...
designSampleSizePTMPlanning future experimental designs of PTM experiments in...
DIANNtoMSstatsPTMFormatConvert the output of DIA-NN PSM file into MSstatsPTM format
dot-calculatePowerPTMPower calculation for PTM experiment
dot-fixTerminusAdd site location and aa
dot-getNumSamplePTMGet sample size for PTM experiment
dot-joinFastaAdd FASTA data into dataframe
dot-locateSitesAdd site location and aa
dot-removeCutoffSitesRemove sites below cutoff probability
fragpipe_annotationExample annotation file for a TMT FragPipe experiment.
fragpipe_annotation_proteinExample annotation file for a global profiling run TMT...
fragpipe_inputOutput of FragPipe TMT PTM experiment
fragpipe_input_proteinOutput of FragPipe TMT global profiling experiment
FragPipetoMSstatsPTMFormatConvert output of TMT labeled Fragpipe data into MSstatsPTM...
groupComparisonPlotsPTMVisualization for model-based analysis and summarization
groupComparisonPTMPerform differential analysis on MS-based proteomics...
locateModLocate modified sites with a peptide
locatePTMAnnotate modified sites with associated peptides
maxq_lf_annotationExample annotation file for a label-free MaxQuant experiment.
maxq_lf_evidenceExample MaxQuant evidence file from the output of a label...
maxq_tmt_annotationExample annotation file for a TMT MaxQuant experiment.
maxq_tmt_evidenceExample MaxQuant evidence file from the output of a TMT...
MaxQtoMSstatsPTMFormatConvert output of label-free or TMT MaxQuant experiments into...
MetamorpheusToMSstatsPTMFormatImport Metamorpheus files into PTM format
MSstatsPTMMSstatsPTM: A package for detecting differentially abundant...
MSstatsPTMSiteLocatorLocate modification site number and amino acid
pd_annotationExample annotation file for a label-free Proteome Discoverer...
pd_psm_inputExample Proteome Discoverer evidence file from the output of...
pd_testing_outputExample output of Proteome Discoverer converter
PDtoMSstatsPTMFormatConvert Proteome Discoverer output into MSstatsPTM format
ProgenesistoMSstatsPTMFormatConverts non-TMT Progenesis output into the format needed for...
PStoMSstatsPTMFormatConvert Peaks Studio output into MSstatsPTM format
raw.inputExample of input PTM dataset for LabelFree/DDA/DIA...
raw.input.tmtExample of input PTM dataset for TMT experiments.
SkylinetoMSstatsPTMFormatConvert Skyline output into MSstatsPTM format
spectronaut_annotationExample annotation file for a label-free Spectronaut...
spectronaut_inputExample Spectronaut evidence file from the output of a label...
SpectronauttoMSstatsPTMFormatConvert Spectronaut output into MSstatsPTM format
summary.dataExample of output from dataSummarizationPTM function for...
summary.data.tmtExample of output from dataSummarizationPTM_TMT function for...
tidyFastaRead and tidy a FASTA file
Vitek-Lab/MSstatsPTM documentation built on Sept. 26, 2024, 9:28 p.m.