Package: phoenics 0.4

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:Camille Guilmineau [aut, cre], Remi Servien [aut], Nathalie Vialaneix [aut]

phoenics_0.4.tar.gz
phoenics_0.4.tar.gz(r-4.5-noble)phoenics_0.4.tar.gz(r-4.4-noble)
phoenics_0.4.tgz(r-4.4-emscripten)phoenics_0.4.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'))

Peer review:

Datasets:

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

1.60 score 148 downloads 7 exports 112 dependencies

Last updated 13 days agofrom:e69bcbb0a4. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 12 2024
R-4.5-linuxOKDec 12 2024

Exports:adjust_pvalextractfrom_ASICS_to_PHOENICSheadoverlap_coefficientpathway_searchtest_pathway

Dependencies:abindbackportsbase64encblmebootbroombslibcachemcarcarDatacliclustercolorspacecorrplotcowplotcpp11crosstalkdendextendDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustfontawesomeFormulafsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplyrpolynompromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangrmarkdownrstatixsassscalesscatterplot3dSparseMstringistringrsurvivaltibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Prepare quantification data from ASICS outputsfrom_ASICS_to_PHOENICS
Dataset "MTBLS422"design MTBLS422 pathways quantif
Calculate overlap coefficient between pathwaysoverlap_coefficient
Query KEGG pathways for a given set of metabolitespathway_search
Class pathwayResadjust_pval adjust_pval.pathwayRes extract extract.pathwayRes head head.pathwayRes pathwayRes plot.pathwayRes print.pathwayRes summary.pathwayRes
Pathway differential analysis based on longitudinal metabolomics datatest_pathway