Package: PepMapViz 1.1.0

Zhenru Zhou

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

A versatile R visualization package that empowers researchers with comprehensive visualization tools for seamlessly mapping peptides to protein sequences, identifying distinct domains and regions of interest, accentuating mutations, and highlighting post-translational modifications, all while enabling comparisons across diverse experimental conditions. Potential applications of 'PepMapViz' include the visualization of cross-software mass spectrometry results at the peptide level for specific protein and domain details in a linearized format and post-translational modification coverage across different experimental conditions; unraveling insights into disease mechanisms. It also enables visualization of Major histocompatibility complex-presented peptide clusters in different antibody regions predicting immunogenicity in antibody drug development.

Authors:Zhenru Zhou [aut, cre], Qui Phung [aut], Corey Bakalarski [aut]

PepMapViz_1.1.0.tar.gz
PepMapViz_1.1.0.tar.gz(r-4.7-any)PepMapViz_1.1.0.tar.gz(r-4.6-any)
PepMapViz_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
PepMapViz/json (API)

# Install 'PepMapViz' in R:

install.packages('PepMapViz', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunogenicity massspectrometry proteomics peptidomics software visualization

2.70 score 1 stars 7 scripts 241 downloads 28 exports 63 dependencies

Last updated from:f357c66dca. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	194
source / vignettes	OK	233
linux-release-x86_64	OK	186
wasm-release	OK	168

Exports:calculate_all_Area calculate_all_PSM calculate_Area calculate_PSM combine_files_from_folder convert_to_regex_pattern create_peptide_plot match_and_calculate_positions obtain_mod obtain_mod_Comet obtain_mod_DIANN obtain_mod_Maxquant obtain_mod_MSFragger obtain_mod_mzIdenML obtain_mod_mzTab obtain_mod_PEAKS obtain_mod_Skyline obtain_mod_Spectronaut peptide_quantification run_pepmap_app strip_sequence strip_sequence_Comet strip_sequence_DIANN strip_sequence_Maxquant strip_sequence_MSFragger strip_sequence_PEAKS strip_sequence_Skyline strip_sequence_Spectronaut

Dependencies:base64enc bslib cachem cli commonmark cpp11 crosstalk data.table digest DT evaluate farver fastmap fontawesome fs ggforce ggh4x ggnewscale ggplot2 glue gtable highr htmltools htmlwidgets httpuv isoband jquerylib jsonlite knitr labeling later lazyeval lifecycle magrittr MASS memoise mime otel polyclip promises R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S7 sass scales shiny sourcetools stringi stringr systemfonts tidyselect tinytex tweenr vctrs viridisLite withr xfun xtable yaml

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

Rendered fromPepMapViz.Rmdusingknitr::rmarkdown

Last update: 2025-06-25
Started: 2024-11-13

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

Package: PepMapViz 1.1.0

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

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)