Package: multiGSEA 1.17.3

Sebastian Canzler

multiGSEA: Combining GSEA-based pathway enrichment with multi omics data integration

Extracted features from pathways derived from 8 different databases (KEGG, Reactome, Biocarta, etc.) can be used on transcriptomic, proteomic, and/or metabolomic level to calculate a combined GSEA-based enrichment score.

Authors:Sebastian Canzler [aut, cre], Jörg Hackermüller [aut]

multiGSEA_1.17.3.tar.gz
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multiGSEA.pdf |multiGSEA.html✨
multiGSEA/json (API)
NEWS

# Install 'multiGSEA' in R:

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

Bug tracker:https://github.com/yigbt/multigsea/issues

Datasets:

metabolome - Metabolomic data set that is used in the toy example provided by the 'multiGSEA' package.
proteome - Proteomic data set that is used in the toy example provided by the 'multiGSEA' package.
transcriptome - Transcriptomic data set that is used in the toy example provided by the 'multiGSEA' package.

On BioConductor:multiGSEA-1.17.3(bioc 3.21)multiGSEA-1.16.2(bioc 3.20)

genesetenrichment pathways reactome biocarta

7.04 score 17 stars 32 scripts 314 downloads 1 mentions 11 exports 112 dependencies

Last updated 2 months agofrom:6b0e4cd281. Checks:6 OK, 1 ERROR. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 06 2025
R-4.5-win	OK	Feb 06 2025
R-4.5-linux	OK	Feb 06 2025
R-4.4-win	OK	Feb 06 2025
R-4.4-mac	OK	Feb 06 2025
R-4.3-win	OK	Feb 06 2025
R-4.3-mac	ERROR	Jan 07 2025

Exports:combinePvalues extractPvalues getFeatures getGeneMapping getMetaboliteMapping getMultiOmicsFeatures getOrganisms initOmicsDataStructure multiGSEA rankFeatures rename_duplicates

Dependencies:AnnotationDbi AnnotationHub askpass BH Biobase BiocFileCache BiocGenerics BiocManager BiocParallel BiocVersion Biostrings bit bit64 blob cachem cli codetools colorspace cowplot cpp11 crayon curl data.table DBI dbplyr DEoptimR dplyr fansi farver fastmap fastmatch fgsea filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData ggplot2 glue graph graphite gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS mathjaxr Matrix MatrixModels memoise metaboliteIDmapping metap mgcv mime mnormt multcomp multtest munsell mutoss mvtnorm nlme numDeriv openssl pillar pkgconfig plogr plotrix png purrr qqconf quantreg R6 rappdirs rbibutils RColorBrewer Rcpp Rdpack rlang robustbase RSQLite S4Vectors sandwich scales sn snow SparseM stringi stringr survival sys TFisher TH.data tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector yaml zoo

multiGSEA: an example workflow

Sebastian Canzler, Jörg Hackermüller

Rendered frommultiGSEA.rmdusingknitr::rmarkdownon Feb 06 2025.

Last update: 2025-01-06
Started: 2020-04-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Retrieve the path to the cache directory.	archiveDir
Retrieve path to a cached file.	archivePath
Calculate a combined p-value for multiple omics layer.	combinePvalues
Create a reshaped data frame from multiGSEA output.	extractPvalues
Wrapper to extract features (nodes) from given pathways.	getFeatures
Mapping between pathway encoded genes/proteins and different ID formats.	getGeneMapping
Get the correct ID mapping database	getIDMappingDatabase
Wrapper to get feature mappings.	getMappedFeatures
Helper function to get all different metabolite ID formats	getMetaboliteIDformats
Mapping between pathway encoded metabolites and different metabolite ID formats.	getMetaboliteMapping
Collect feature mapping for user given databases and omics layer.	getMultiOmicsFeatures
Get list of supported organisms	getOrganisms
Create an empty data structure for measured omics features	initOmicsDataStructure
Read a local RDS file.	loadLocal
Helper function to map only a subset of metabolite IDs	mapIDType
Metabolomic data set that is used in the toy example provided by the `multiGSEA` package.	metabolome
Calculate pathway enrichment for multiple omics layer.	multiGSEA
Proteomic data set that is used in the toy example provided by the `multiGSEA` package.	proteome
Pre-rank features prior to calculating enrichment scores.	rankFeatures
Make a list of strings unique	rename_duplicates
Transcriptomic data set that is used in the toy example provided by the `multiGSEA` package.	transcriptome