Package: funOmics 0.99.8

Elisa Gomez de Lope

funOmics: Aggregating Omics Data into Higher-Level Functional Representations

The 'funOmics' package ggregates or summarizes omics data into higher level functional representations such as GO terms gene sets or KEGG metabolic pathways. The aggregated data matrix represents functional activity scores that facilitate the analysis of functional molecular sets while allowing to reduce dimensionality and provide easier and faster biological interpretations. Coordinated functional activity scores can be as informative as single molecules!

Authors:Elisa Gomez de Lope [aut, cre], Enrico Glaab [ctb]

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funOmics.pdf |funOmics.html✨
funOmics/json (API)
NEWS

# Install 'funOmics' in R:

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

Bug tracker:https://github.com/elisagdelope/funomics/issues

On BioConductor:funOmics-0.99.8(bioc 3.20)

bioconductor-package

3 exports 0.82 score 83 dependencies

Last updated 2 months agofrom:5d40c695f2

Exports:get_kegg_sets short_sets_detail summarize_pathway_level

Dependencies:AnnotationDbi askpass Biobase BiocGenerics BiocManager Biostrings bit bit64 blob cachem cli cluster codetools colorspace cpp11 crayon curl DBI digest doParallel dplyr fansi farver fastmap foreach generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gridBase gtable httr IRanges isoband iterators jsonlite KEGGREST labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme NMF openssl org.Hs.eg.db pathifier pillar pkgconfig plogr plyr png princurve R.methodsS3 R.oo R6 RColorBrewer Rcpp registry reshape2 rlang rngtools RSQLite S4Vectors scales stringi stringr sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

funOmics

Elisa Gómez de Lope

Rendered fromfunomics_vignette.Rmdusingknitr::rmarkdownon Jun 13 2024.

Last update: 2024-05-15
Started: 2024-02-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Aggregating Omics Data into Higher-Level Functional Representations	funOmics-package funOmics
Retrieves KEGG pathway gene sets for a specified organism and gene ID type.	get_kegg_sets
Retrieve details and information about short molecular sets	short_sets_detail
Aggregates or summarizes omics data into higher-level functional representations that can be interpreted as functional activity scores or measures.	summarize_pathway_level