Package: FELLA 1.27.0

Sergio Picart-Armada

FELLA: Interpretation and enrichment for metabolomics data

Enrichment of metabolomics data using KEGG entries. Given a set of affected compounds, FELLA suggests affected reactions, enzymes, modules and pathways using label propagation in a knowledge model network. The resulting subnetwork can be visualised and exported.

Authors:Sergio Picart-Armada [aut, cre], Francesc Fernandez-Albert [aut], Alexandre Perera-Lluna [aut]

FELLA_1.27.0.tar.gz
FELLA_1.27.0.zip(r-4.5)FELLA_1.27.0.zip(r-4.4)FELLA_1.27.0.zip(r-4.3)
FELLA_1.27.0.tgz(r-4.4-any)FELLA_1.27.0.tgz(r-4.3-any)
FELLA_1.27.0.tar.gz(r-4.5-noble)FELLA_1.27.0.tar.gz(r-4.4-noble)
FELLA_1.27.0.tgz(r-4.4-emscripten)FELLA_1.27.0.tgz(r-4.3-emscripten)
FELLA.pdf |FELLA.html✨
FELLA/json (API)
NEWS

# Install 'FELLA' in R:
install.packages('FELLA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:FELLA-1.27.0(bioc 3.21)FELLA-1.26.0(bioc 3.20)

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

softwaremetabolomicsgraphandnetworkkegggopathwaysnetworknetworkenrichment

5.90 score 25 scripts 282 downloads 8 mentions 31 exports 34 dependencies

Last updated 2 months agofrom:d1ba32c979. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winNOTENov 20 2024
R-4.5-linuxNOTENov 20 2024
R-4.4-winNOTENov 20 2024
R-4.4-macNOTENov 20 2024
R-4.3-winNOTENov 20 2024
R-4.3-macNOTENov 20 2024

Exports:addGOToGraphbuildDataFromGraphbuildGraphFromKEGGRESTdefineCompoundsenrichexportResultsgenerateEnzymesTablegenerateResultsGraphgenerateResultsTablegetBackgroundgetComgetExcludedgetGraphgetInfogetInputgetNamegetPscoresis.FELLA.DATAis.FELLA.USERlaunchApplistApproxlistCategorieslistInternalDatabaseslistMethodsloadKEGGdataplotplotGraphrunDiffusionrunHypergeomrunPagerankshow

Dependencies:askpassBiocGenericsBiostringsclicpp11crayoncurlgenericsGenomeInfoDbGenomeInfoDbDatagluehttrigraphIRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmimeopensslpkgconfigplyrpngR6RcpprlangS4VectorssysUCSC.utilsvctrsXVectorzlibbioc

A fatty liver study on Mus musculus

Sergio Picart-Armada, Alexandre Perera-Lluna

Rendered frommusmusculus.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2018-09-24
Started: 2018-09-18

An oxybenzone exposition study on gilt-head bream

Sergio Picart-Armada, Alexandre Perera-Lluna

Rendered fromzebrafish.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2018-09-24
Started: 2018-09-18

FELLA

Rendered fromFELLA.Rnwusingutils::Sweaveon Nov 20 2024.

Last update: 2019-02-15
Started: 2018-01-02

An overview of FELLA: data enrichment for metabolomics summary data

Sergio Picart-Armada, Alexandre Perera-Lluna

Rendered fromquickstart.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2017-09-01
Started: 2017-08-31

Readme and manuals

Help Manual

Help pageTopics
An internal S4 class for the diffusion dataD.diffusion-class
An internal S4 class for the binary matrix (hypergeometric test)D.hypergeom-class
An internal S4 class to represent the KEGG graph and related filesD.keggdata-class
An internal S4 class for the PageRank dataD.pagerank-class
Parse, build and load the KEGG knowledge modelbuildDataFromGraph buildGraphFromKEGGREST data-funs loadKEGGdata
Functions to map and enrich a list of metabolitesdefineCompounds enrich enrich-funs runDiffusion runHypergeom runPagerank
Generate and manipulate tables and sub-networks from an enrichmentaddGOToGraph export-funs exportResults generateEnzymesTable generateResultsGraph generateResultsTable plotGraph
The FELLA packageFELLA-package FELLA
An S4 class to represent all the necessary KEGG dataFELLA.DATA FELLA.DATA-class show,FELLA.DATA-method
FELLA.DATA sample dataFELLA.sample
An S4 class to save all the user analysis dataFELLA.USER FELLA.USER-class plot,FELLA.USER,missing-method show,FELLA.USER-method
Get compounds in the defined backgroundgetBackground
Get communitygetCom
Get excluded compoundsgetExcluded
Get KEGG graphgetGraph
Get KEGG version infogetInfo
Get metabolites in the inputgetInput
Get matrix for the desired methodologygetMatrix
Map KEGG identifiers to KEGG namesgetName
Get p-scores from the desired methodologygetPscores
Get the slot "status"getStatus
Get rowSums/squaredRowSumsgetSums
Get the slot "valid"getValid
A randomly generated list of affected metabolitesinput.sample
Check FELLA.DATA classis.FELLA.DATA
Check FELLA.USER classis.FELLA.USER
Launch a shiny app with FELLAlaunchApp
List of approximationslistApprox
List of node categorieslistCategories
List internal databaseslistInternalDatabases
List of methodslistMethods
Internal function to add a legend to a graph plotplotLegend
An internal S4 class for the user data of the diffusion enrichment analysisU.diffusion-class
An internal S4 class for the user data of the hypergeometric over representation analysisU.hypergeom-class
An internal S4 class for the user data of the PageRank enrichment analysisU.pagerank-class
An internal S4 class for the user input dataU.userinput-class