Package: multiGSEA 1.23.0

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_1.23.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
multiGSEA/json (API)

# 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-1.23.0(bioc 3.24)multiGSEA-1.22.0(bioc 3.23)

genesetenrichment pathways reactome biocarta

6.68 score 22 stars 44 scripts 1 mentions 11 exports 108 dependencies

Last updated from:1d8d9841f8. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	496
linux-devel-x86_64	OK	844
source / vignettes	OK	1307
linux-release-x86_64	OK	806
macos-release-arm64	OK	558
macos-oldrel-arm64	OK	481
windows-devel	OK	1698
windows-release	OK	1674
windows-oldrel	OK	1489
wasm-release	OK	408

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

Dependencies:AnnotationDbi AnnotationHub askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocParallel BiocVersion Biostrings bit bit64 blob cachem cli codetools cowplot cpp11 crayon curl data.table DBI dbplyr DEoptimR dir.expiry dplyr farver fastmap fastmatch fgsea filelock formatR futile.logger futile.options generics ggplot2 glue graph graphite gtable httr httr2 IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS mathjaxr Matrix MatrixModels memoise metaboliteIDmapping metap mime mnormt multcomp multtest mutoss mvtnorm numDeriv openssl pillar pkgconfig plotrix png purrr qqconf quantreg R6 rappdirs rbibutils RColorBrewer Rcpp Rdpack rlang robustbase RSQLite S4Vectors S7 sandwich scales Seqinfo sn snow SparseM stringi stringr survival sys TFisher TH.data tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector yaml zoo

multiGSEA: an example workflow

Rendered frommultiGSEA.rmdusingknitr::rmarkdown

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