Package: phoenics 0.3
Camille Guilmineau
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 is based on a Principal Component Analysis step and on a linear mixed model. Automatic query of metabolic pathways is also implemented.
Authors:
phoenics_0.3.tar.gz
phoenics_0.3.tar.gz(r-4.5-noble)phoenics_0.3.tar.gz(r-4.4-noble)
phoenics_0.3.tgz(r-4.4-emscripten)phoenics_0.3.tgz(r-4.3-emscripten)
phoenics.pdf |phoenics.html✨
phoenics/json (API)
NEWS
| # 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 4 months agofrom:27d8a69c86. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 20 2024 |
| R-4.5-linux | OK | Nov 20 2024 |
Exports:adjust_pvalextractfrom_ASICS_to_PHOENICSheadoverlap_coefficientpathway_searchtest_pathway
Dependencies:abindbackportsbase64encblmebootbroombslibcachemcarcarDatacliclustercolorspacecorrplotcowplotcpp11crosstalkdendextendDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustfontawesomeFormulafsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplyrpolynompromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangrmarkdownrstatixsassscalesscatterplot3dSparseMstringistringrsurvivaltibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyaml
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 head.pathwayRes pathwayRes plot.pathwayRes print.pathwayRes summary.pathwayRes |
| Pathway differential analysis based on longitudinal metabolomics data | test_pathway |