Package: EGSEA 1.35.0

Monther Alhamdoosh

EGSEA: Ensemble of Gene Set Enrichment Analyses

This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. EGSEA algorithm utilizes the analysis results of twelve prominent GSE algorithms in the literature to calculate collective significance scores for each gene set.

Authors:Monther Alhamdoosh [aut, cre], Luyi Tian [aut], Milica Ng [aut], Matthew Ritchie [ctb]

EGSEA_1.35.0.tar.gz
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EGSEA.pdf |EGSEA.html✨
EGSEA/json (API)
NEWS

# Install 'EGSEA' in R:

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

Datasets:

arraydata - Example dataset for 'egsea.ma'

On BioConductor:EGSEA-1.35.0(bioc 3.21)EGSEA-1.34.0(bioc 3.20)

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

immunooncology differentialexpression go geneexpression genesetenrichment genetics microarray multiplecomparison onechannel pathways rnaseq sequencing software systemsbiology twochannel metabolomics proteomics kegg graphandnetwork genesignaling genetarget networkenrichment network classification

6.09 score 62 scripts 512 downloads 22 mentions 31 exports 190 dependencies

Last updated 2 months agofrom:bc1e9883ad. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 27 2024
R-4.5-win	NOTE	Nov 27 2024
R-4.5-linux	NOTE	Nov 27 2024
R-4.4-win	NOTE	Nov 27 2024
R-4.4-mac	NOTE	Nov 27 2024
R-4.3-win	NOTE	Nov 27 2024
R-4.3-mac	NOTE	Nov 27 2024

Exports:buildCustomIdx buildGeneSetDBIdx buildGMTIdx buildIdx buildKEGGIdx buildMSigDBIdx egsea egsea.base egsea.cnt egsea.combine egsea.logo egsea.ma egsea.ora egsea.sort generateReport getlimmaResults getSetByID getSetByName getSetScores limmaTopTable plotBars plotGOGraph plotHeatmap plotMethods plotPathway plotSummary plotSummaryHeatmap show showSetByID showSetByName topSets

Dependencies:abind annotate AnnotationDbi askpass assorthead base64enc beachmat BH Biobase BiocFileCache BiocGenerics BiocParallel BiocSingular Biostrings bit bit64 bitops blob bslib cachem caTools cli codetools colorspace cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats DEoptimR digest doRNG dplyr DT edgeR EGSEAdata evaluate fansi farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options gage generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 globaltest glue GO.db gplots graph GSA GSEABase GSVA gtable gtools HDF5Array hgu133a.db hgu133plus2.db highr htmltools HTMLUtils htmlwidgets httpuv httr hwriter IRanges irlba isoband iterators jquerylib jsonlite KEGGdzPathwaysGEO KEGGgraph KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magick magrittr MASS mathjaxr Matrix MatrixGenerics MatrixModels matrixStats memoise metap mgcv mime mnormt multcomp multtest munsell mutoss mvtnorm nlme numDeriv openssl org.Hs.eg.db org.Mm.eg.db org.Rn.eg.db PADOG pathview pillar pkgconfig plogr plotly plotrix png promises purrr qqconf quantreg R2HTML R6 rappdirs rbibutils RColorBrewer Rcpp RCurl Rdpack Rgraphviz rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown rngtools robustbase RSQLite rsvd S4Arrays S4Vectors safe sandwich sass ScaledMatrix scales SingleCellExperiment sn snow SparseArray SparseM sparseMatrixStats SpatialExperiment statmod stringi stringr SummarizedExperiment survival sys TFisher TH.data tibble tidyr tidyselect tinytex topGO UCSC.utils utf8 vctrs viridisLite withr xfun XML xtable XVector yaml zlibbioc zoo

EGSEA vignette

Rendered fromEGSEA.Rnwusingknitr::knitron Nov 27 2024.

Last update: 2018-07-25
Started: 2016-04-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Ensemble of Gene Enrichment Analysis (EGSEA)	EGSEA-package EGSEA
Example dataset for 'egsea.ma'	arraydata
Functions to create gene set collection indexes for EGSEA	buildCustomIdx buildCustomIdx,egsea-index buildGeneSetDBIdx buildGeneSetDBIdx,egsea-index buildGMTIdx buildGMTIdx,egsea-index buildIdx buildIdx,egsea-index buildKEGGIdx buildKEGGIdx,egsea-index buildMSigDBIdx buildMSigDBIdx,egsea-index
Core functions to perform ensemble of gene set enrichment analysis (EGSEA)	egsea egsea,egsea-main egsea.cnt egsea.cnt,egsea-main egsea.ma egsea.ora egsea.ora,egsea-main
EGSEA auxiliary functions	egsea.base egsea.base,egsea-aux egsea.combine egsea.combine,egsea-aux egsea.logo egsea.logo,egsea-aux egsea.sort egsea.sort,egsea-aux
The EGSEAResults class	$,EGSEAResults-method EGSEAResults EGSEAResults-class generateReport generateReport,EGSEAResults-method getlimmaResults getlimmaResults,EGSEAResults-method getSetScores getSetScores,EGSEAResults-method limmaTopTable limmaTopTable,EGSEAResults-method plotBars plotBars,EGSEAResults-method plotGOGraph plotGOGraph,EGSEAResults-method plotHeatmap plotHeatmap,EGSEAResults-method plotMethods plotMethods,EGSEAResults-method plotPathway plotPathway,EGSEAResults-method plotSummary plotSummary,EGSEAResults-method plotSummaryHeatmap plotSummaryHeatmap,EGSEAResults-method show,EGSEAResults-method showSetByID showSetByID,EGSEAResults-method showSetByName showSetByName,EGSEAResults-method summary,EGSEAResults-method topSets topSets,EGSEAResults-method
The GSCollectionIndex class	$,GSCollectionIndex-method getSetByID getSetByID,GSCollectionIndex-method getSetByName getSetByName,GSCollectionIndex-method GSCollectionIndex GSCollectionIndex-class show,GSCollectionIndex-method summary,GSCollectionIndex-method