R: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration

# A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration

## Documentation for package ‘PepMapViz’ version 1.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

calculate_all_Area | Calculate Area/Intensity for the whole input sequence dataframe
calculate_all_PSM | Calculate Spectra Count (PSM) for the whole input sequence dataframe
calculate_Area | Calculate Area/Intensity for one row of the input sequence dataframe
calculate_PSM | Calculate Spectra Count (PSM) for one row of the input sequence dataframe
combine_files_from_folder | Combine CSV and TXT Files from a Folder
convert_to_regex_pattern | Convert Peptide Sequence to Regex Pattern
create_peptide_plot | Create a peptide Plot
match_and_calculate_positions | Match peptide sequence with provided sequence and calculate positions
obtain_mod | Obtain post translational modification(PTM) information from Peptide data based on the specified data type
obtain_mod_Comet | Obtain modification information from Peptide data generated by Comet
obtain_mod_DIANN | Obtain modification information from Peptide data generated by DIA-NN
obtain_mod_Maxquant | Obtain modification information from Peptide data generated by Maxquant
obtain_mod_MSFragger | Obtain modification information from Peptide data generated by MSFragger
obtain_mod_mzIdenML | Obtain modification information from Peptide data generated by mzIdenML
obtain_mod_mzTab | Obtain modification information from Peptide data generated by mzTab
obtain_mod_PEAKS | Obtain modification information from Peptide data generated by PEAKS
obtain_mod_Skyline | Obtain modification information from Peptide data generated by Skyline
obtain_mod_Spectronaut | Obtain modification information from Peptide data generated by Spectronaut
peptide_quantification | Peptide Quantification
run_pepmap_app | Launch PepMapViz Shiny Application
strip_sequence | Strip peptide sequences based on the specified data type
strip_sequence_Comet | Strip sequence from Comet outputs
strip_sequence_DIANN | Strip sequence from DIANN outputs
strip_sequence_Maxquant | Strip sequence from Maxquant outputs
strip_sequence_MSFragger | Strip sequence from MSFragger outputs
strip_sequence_PEAKS | Strip sequence from PEAKS outputs
strip_sequence_Skyline | Strip sequence from Skyline outputs
strip_sequence_Spectronaut | Strip sequence from Spectronaut outputs