Package: PepMapViz 1.0.0

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 peptides in different antibody regions predicting immunogenicity in antibody drug development.

Authors:Zhenru Zhou [aut, cre], Qui Phung [ctb], Corey Bakalarski [aut], Genentech, Inc. [cph]

PepMapViz_1.0.0.tar.gz
PepMapViz_1.0.0.tar.gz(r-4.5-noble)PepMapViz_1.0.0.tar.gz(r-4.4-noble)
PepMapViz_1.0.0.tgz(r-4.4-emscripten)PepMapViz_1.0.0.tgz(r-4.3-emscripten)
PepMapViz.pdf |PepMapViz.html✨
PepMapViz/json (API)

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

Peer review:

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

immunogenicitymassspectrometryproteomicspeptidomicssoftwarevisualization

2.70 score 4 scripts 495 downloads 25 exports 41 dependencies

Last updated 1 months agofrom:c8a075774e. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 14 2024
R-4.5-linuxOKDec 14 2024

Exports:calculate_all_Areacalculate_all_PSMcalculate_Areacalculate_PSMcombine_files_from_folderconvert_to_regex_patterncreate_peptide_plotmatch_and_calculate_positionsobtain_modobtain_mod_Cometobtain_mod_DIANNobtain_mod_Maxquantobtain_mod_MSFraggerobtain_mod_PEAKSobtain_mod_Skylineobtain_mod_Spectronautpeptide_quantificationstrip_sequencestrip_sequence_Cometstrip_sequence_DIANNstrip_sequence_Maxquantstrip_sequence_MSFraggerstrip_sequence_PEAKSstrip_sequence_Skylinestrip_sequence_Spectronaut

Dependencies:clicolorspacecpp11data.tablefansifarverggforceggh4xggnewscaleggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpolyclipR6RColorBrewerRcppRcppEigenrlangscalesstringistringrsystemfontstibbletidyselecttweenrutf8vctrsviridisLitewithr

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

Zhenru Zhou [email protected], Qui Phung [email protected], Corey Bakalarski [email protected]

Rendered fromPepMapViz.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2024-11-13
Started: 2024-11-13

Readme and manuals

Help Manual

Help pageTopics
Calculate Area/Intensity for the whole input sequence dataframecalculate_all_Area
Calculate Spectra Count (PSM) for the whole input sequence dataframecalculate_all_PSM
Calculate Area/Intensity for one row of the input sequence dataframecalculate_Area
Calculate Spectra Count (PSM) for one row of the input sequence dataframecalculate_PSM
Combine CSV and TXT Files from a Foldercombine_files_from_folder
Convert Peptide Sequence to Regex Patternconvert_to_regex_pattern
Create a peptide Plotcreate_peptide_plot
Match peptide sequence with provided sequence and calculate positionsmatch_and_calculate_positions
Obtain post translational modification(PTM) information from Peptide data based on the specified data typeobtain_mod
Obtain modification information from Peptide data generated by Cometobtain_mod_Comet
Obtain modification information from Peptide data generated by DIA-NNobtain_mod_DIANN
Obtain modification information from Peptide data generated by Maxquantobtain_mod_Maxquant
Obtain modification information from Peptide data generated by MSFraggerobtain_mod_MSFragger
Obtain modification information from Peptide data generated by PEAKSobtain_mod_PEAKS
Obtain modification information from Peptide data generated by Skylineobtain_mod_Skyline
Obtain modification information from Peptide data generated by Spectronautobtain_mod_Spectronaut
Peptide Quantificationpeptide_quantification
Strip peptide sequences based on the specified data typestrip_sequence
Strip sequence from Comet outputsstrip_sequence_Comet
Strip sequence from DIANN outputsstrip_sequence_DIANN
Strip sequence from Maxquant outputsstrip_sequence_Maxquant
Strip sequence from MSFragger outputsstrip_sequence_MSFragger
Strip sequence from PEAKS outputsstrip_sequence_PEAKS
Strip sequence from Skyline outputsstrip_sequence_Skyline
Strip sequence from Spectronaut outputsstrip_sequence_Spectronaut