Introduction | MTBLS422 dataset | phoenics test | Perform test | Access test results | Explore PCA results | Options of phoenics main test function | Switching from PCA to MFA | Wrapper to automatically query pathways | References | Session information
This package is considered a duplicate. The official version of this package is found at:https://r-serv.r-universe.dev/phoenics
Package: phoenics 0.6.1
Remi Servien
phoenics: Pathways Longitudinal and Differential Analysis in Metabolomics
Perform a differential analysis at pathway level based on metabolite quantifications and information on pathway metabolite composition. The method, described in Guilmineau et al (2025) <doi:10.1186/s12859-025-06118-z> is based on a Principal Component Analysis step and on a linear mixed model. Automatic query of metabolic pathways is also implemented.
Authors:
phoenics_0.6.1.tar.gz
phoenics_0.6.1.tar.gz(r-4.7-any)phoenics_0.6.1.tar.gz(r-4.6-any)
phoenics_0.6.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phoenics/json (API)
| # Install 'phoenics' in R: |
| install.packages('phoenics', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:fb723851ca. Checks:4 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 193 | ||
| source / vignettes | OK | 224 | ||
| linux-release-x86_64 | OK | 188 | ||
| wasm-release | OK | 180 |
Exports:adjust_pvalextractfrom_ASICS_to_PHOENICSoverlap_coefficientpathway_searchtest_pathway
Dependencies:abindbackportsbase64encblmebootbroombslibcachemcarcarDatacliclustercolorspacecorrplotcowplotcpp11crosstalkdendextendDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluatefactoextraFactoMineRfarverfastmapflashClustfontawesomeforecastFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetsirlbaisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmemoisemgcvmimeminqamodelrmultcompViewmvtnormnlmenloptrnnetnumDerivotelpbkrtestpillarpkgconfigpolynompromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownrstatixS7sassscalesscatterplot3dSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisviridisLitewithrxfunyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Prepare quantification data from ASICS outputs | from_ASICS_to_PHOENICS |
| Dataset "MTBLS422" | design MTBLS422 pathways quantif |
| Calculate overlap coefficient between pathways | overlap_coefficient |
| Query KEGG pathways for a given set of metabolites | pathway_search |
| Class pathwayRes | adjust_pval adjust_pval.pathwayRes extract extract.pathwayRes head.pathwayRes pathwayRes plot.pathwayRes print.pathwayRes summary.pathwayRes |
| Pathway differential analysis based on longitudinal metabolomics data | test_pathway |
