1 Introduction | 2 Example data | 3 Singular Enrichment analysis (SEA) | 3.1 Enrichment | 3.2 Plotting SEA results | 4 Protein set enrichment analysis (PSEA) | 4.1 PSEA | 4.2 Plotting | 5. Translate PEIMAN results for Mass spectrometry searching tools | References
Package: PEIMAN2 1.1.0
PEIMAN2: Post-Translational Modification Enrichment, Integration, and Matching Analysis
Functions and mined database from 'UniProt' focusing on post-translational modifications to do single enrichment analysis (SEA) and protein set enrichment analysis (PSEA). Payman Nickchi, Uladzislau Vadadokhau, Mehdi Mirzaie, Marc Baumann, Amir Ata Saei, Mohieddin Jafari (2025) <doi:10.1002/pmic.202400238>.
Authors:
PEIMAN2_1.1.0.tar.gz
PEIMAN2_1.1.0.zip(r-4.7)PEIMAN2_1.1.0.zip(r-4.6)PEIMAN2_1.1.0.zip(r-4.5)
PEIMAN2_1.1.0.tgz(r-4.6-any)PEIMAN2_1.1.0.tgz(r-4.5-any)
PEIMAN2_1.1.0.tar.gz(r-4.7-any)PEIMAN2_1.1.0.tar.gz(r-4.6-any)
PEIMAN2_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
PEIMAN2/json (API)
| # Install 'PEIMAN2' in R: |
| install.packages('PEIMAN2', repos = c('https://pnickchi.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pnickchi/peiman2/issues
Datasets:
- exmplData1 - Example dataset1
- exmplData2 - Example dataset 2
- mod_ont - Database of protein modifications
- ptmlist - Controlled vocabulary for post-translational modifications (PTM) terms
Last updated from:04de2f117a. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 181 | ||
| source / vignettes | OK | 357 | ||
| linux-release-x86_64 | NOTE | 190 | ||
| macos-release-arm64 | NOTE | 140 | ||
| macos-oldrel-arm64 | NOTE | 133 | ||
| windows-devel | NOTE | 200 | ||
| windows-release | NOTE | 121 | ||
| windows-oldrel | NOTE | 158 | ||
| wasm-release | OK | 123 |
Exports:getTaxonomyNameplotEnrichmentplotPSEAplotRunningScorepsea2massrunEnrichmentrunPSEAsea2massupdate_peiman_database
Dependencies:clicpp11dplyrfarverforcatsgenericsggplot2gluegtableisobandjsonlitelabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesstringistringrtibbletidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Example dataset1 | exmplData1 |
| Example dataset 2 | exmplData2 |
| Return the exact taxonomy name for list of protein | getTaxonomyName |
| Database of protein modifications | mod_ont |
| Plot and match singular enrichment results | plotEnrichment |
| Plot the results of protein set enrichment analysis (PSEA) | plotPSEA |
| Plot running score plot for the results of psea | plotRunningScore |
| Translate PSEA results for Mass Spectrometry searching tools | psea2mass |
| Controlled vocabulary for post-translational modifications (PTM) terms | ptmlist |
| Run singular enrichment analysis (SEA) for a given list of protein | runEnrichment |
| Run Protein Set Enrichment Analysis (PSEA) | runPSEA |
| Translate SEA results for Mass Spectrometry searching tools | sea2mass |
| Download and cache PEIMAN2 external data files | update_peiman_database |
