Package index
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DIANNtoMSstatsPTMFormat() - Convert the output of DIA-NN PSM file into MSstatsPTM format
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FragPipetoMSstatsPTMFormat() - Convert output of TMT labeled Fragpipe data into MSstatsPTM format.
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MSstatsPTMSiteLocator() - Locate modification site number and amino acid
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MaxQtoMSstatsPTMFormat() - Convert output of label-free or TMT MaxQuant experiments into MSstatsPTM format
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MetamorpheusToMSstatsPTMFormat() - Import Metamorpheus files into PTM format
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PDtoMSstatsPTMFormat() - Convert Proteome Discoverer output into MSstatsPTM format
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PStoMSstatsPTMFormat() - Convert Peaks Studio output into MSstatsPTM format
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ProgenesistoMSstatsPTMFormat() - Converts non-TMT Progenesis output into the format needed for MSstatsPTM
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ProteinProspectortoMSstatsPTMFormat() - Generate MSstatsPTM required input format from Protein Prospector output
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SkylinetoMSstatsPTMFormat() - Convert Skyline output into MSstatsPTM format
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SpectronauttoMSstatsPTMFormat() - Convert Spectronaut output into MSstatsPTM format
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annotSite() - Annotate modification site
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dataProcessPTM() - Data processing and summarization of peptide-level quantification to PTM and protein level quantification
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dataProcessPlotsPTM() - Visualization for explanatory data analysis
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dataSummarizationPTM() - Data summarization function for label-free MS experiments targeting PTMs.
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dataSummarizationPTM_TMT() - Data summarization function for TMT labelled MS experiments targeting PTMs.
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designSampleSizePTM() - Planning future experimental designs of PTM experiments in sample size calculation
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.fixTerminus() - Fix terminus location adjustments
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fragpipe_annotation - Example annotation file for a TMT FragPipe experiment.
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fragpipe_annotation_protein - Example annotation file for a global profiling run TMT FragPipe experiment.
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fragpipe_input - Output of FragPipe TMT PTM experiment
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fragpipe_input_protein - Output of FragPipe TMT global profiling experiment
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groupComparisonPTM() - Perform differential analysis on MS-based proteomics experiments targeting PTMs
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groupComparisonPlotsPTM() - Visualization for model-based analysis and summarization
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locateMod() - Locate modified sites with a peptide
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locatePTM() - Annotate modified sites with associated peptides
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maxq_lf_annotation - Example annotation file for a label-free MaxQuant experiment.
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maxq_lf_evidence - Example MaxQuant evidence file from the output of a label free experiment
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maxq_tmt_annotation - Example annotation file for a TMT MaxQuant experiment.
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maxq_tmt_evidence - Example MaxQuant evidence file from the output of a TMT experiment
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pd_annotation - Example annotation file for a label-free Proteome Discoverer experiment.
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pd_psm_input - Example Proteome Discoverer evidence file from the output of a label free experiment
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pd_testing_output - Example output of Proteome Discoverer converter
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raw.input - Example of input PTM dataset for LabelFree/DDA/DIA experiments.
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raw.input.tmt - Example of input PTM dataset for TMT experiments.
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spectronaut_annotation - Example annotation file for a label-free Spectronaut experiment.
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spectronaut_input - Example Spectronaut evidence file from the output of a label free experiment
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summary.data - Example of output from dataSummarizationPTM function for non-TMT data
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summary.data.tmt - Example of output from dataSummarizationPTM_TMT function for TMT data
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tidyFasta() - Read and tidy a FASTA file