Package: PEIMAN2 0.1.0

Payman Nickchi

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, Mehdi Mirzaie, Marc Baumann, Amir Ata Saei, Mohieddin Jafari (2022) <bioRxiv:10.1101/2022.11.09.515610>.

Authors:Mohieddin Jafari [aut], Payman Nickchi [aut, cre]

PEIMAN2_0.1.0.tar.gz
PEIMAN2_0.1.0.tar.gz(r-4.5-noble)PEIMAN2_0.1.0.tar.gz(r-4.4-noble)
PEIMAN2_0.1.0.tgz(r-4.4-emscripten)PEIMAN2_0.1.0.tgz(r-4.3-emscripten)
PEIMAN2.pdf |PEIMAN2.html✨
PEIMAN2/json (API)

# Install 'PEIMAN2' in R:

install.packages('PEIMAN2', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

exmplData1 - Example dataset1
exmplData2 - Example dataset 2
mod_ont - Database of protein modifications
ptmlist - Controlled vocabulary for post-translational modifications (PTM) terms

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

2.70 score 6 scripts 162 downloads 8 exports 106 dependencies

Last updated 2 years agofrom:166f17aad5. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 15 2024
R-4.5-linux	OK	Dec 15 2024

Exports:getTaxonomyName plotEnrichment plotPSEA plotRunningScore psea2mass runEnrichment runPSEA sea2mass

Dependencies:askpass backports base64enc bit bit64 blob broom bslib cachem callr cellranger cli clipr colorspace conflicted cpp11 crayon curl data.table DBI dbplyr digest dplyr dtplyr evaluate fansi farver fastmap fontawesome forcats fs gargle generics ggplot2 glue googledrive googlesheets4 gtable haven highr hms htmltools httr ids isoband jquerylib jsonlite knitr labeling lattice lifecycle lubridate magrittr MASS Matrix memoise mgcv mime modelr munsell nlme openssl pillar pkgconfig prettyunits processx progress ps purrr R6 ragg rappdirs RColorBrewer readr readxl rematch rematch2 reprex rlang rmarkdown rstudioapi rvest sass scales selectr stringi stringr sys systemfonts textshaping tibble tidyr tidyselect tidyverse timechange tinytex tzdb utf8 uuid vctrs viridisLite vroom withr xfun xml2 yaml

PEIMAN2-vignette

Payman Nickchi, Mohieddin Jafari

Rendered fromPEIMAN2-vignette.Rmdusingknitr::rmarkdownon Dec 15 2024.

Last update: 2022-11-21
Started: 2022-11-21

Citation

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