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GSEABase specifications


Unique identifier OMICS_29378
Name GSEABase
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.42.0
Stability Stable
AnnotationDbi, methods, testthat, R(>=2.6.0), GO.db,, Rgraphviz, hgu95av2.db, Biobase(>=2.17.8), XML, BiocGenerics(>=0.13.8), ReportingTools, annotate(>=1.45.3), graph(>=1.37.2)
Maintained Yes




No version available


Additional information

GSEABase citations


Innate Immune Response and Off Target Mis splicing Are Common Morpholino Induced Side Effects in Xenopus

Dev Cell
PMCID: 5861998
PMID: 29478923
DOI: 10.1016/j.devcel.2018.01.022

[…] wo Venn diagrams (C) for elevated and reduced transcript levels using limma v3.30.13 (). The five largest Venn fields were analyzed for enriched biological processes (BP) using GOstats v2.40.0 () and GSEABase (). Gene-specific BP term associations were previously generated using BLAST2GO (, , ). Parental, regulatory and component relationships between enriched BP were visualized as ‘perturbation n […]


Transcriptome analysis reveals mechanisms of geroprotective effects of fucoxanthin in Drosophila

BMC Genomics
PMCID: 5836829
PMID: 29504896
DOI: 10.1186/s12864-018-4471-x
call_split See protocol

[…] s) Pathways database was used to find pathways in which the differentially expressed genes are involved []. The GSEA (gene set enrichment analysis) analysis was performed using the software package R GSEAbase of Bioconductor []. […]


R Script Approach to Infer Toxoplasma Infection Mechanisms From Microarrays and Domain Domain Protein Interactions

Bioinform Biol Insights
PMCID: 5753922
PMID: 29317802
DOI: 10.1177/1177932217747256

[…] other pathogen-host coexpression experiments to predict more PHI for specific domains. Our R script does not seek to compete with other approaches, such as GSEA, or other R packages, such as limma or GSEABase,; rather, we wrote an R script code to identify plausible pathogen genes involved in pathogenesis, particularly those with high expression variability. Furthermore, using their functional dom […]


Large scale bioactivity analysis of the small molecule assayed proteome

PLoS One
PMCID: 5298297
PMID: 28178331
DOI: 10.1371/journal.pone.0171413

[…] e obtained from InterPro []. The subset of GO slim terms (Generic version) was obtained from the GO Consortium. Hypergeometric GO term enrichment tests were performed using the R language GOstats and GSEABase packages []. […]


TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

PMCID: 5302158
PMID: 28232861
DOI: 10.5256/f1000research.9601.r14695

[…] KernSmooth _ 2.23–15 108 [71] doRNG _ 1.6 shape _ 1.4.2 109 [73] stringr _ 1.0.0 qvalue _ 2.4.2 110 [75] nor1mix _ 1.2–1 coin _ 1.1–2 111 [77] ShortRead _ 1.30.0 scales _ 0.4.0 112 [79] GSEABase _ 1.34.0 magrittr _ 1.5 113 [81] plyr _ 1.8.4 gdata _ 2.17.0 114 [83] zlibbioc _ 1.18.0 RColorBrewer _ 1.1–2 115 [85] illuminaio _ 0.14.0 plotrix _ 3.6–3 116 [87] KEGGgraph _ 1.30.0 […]


Transcriptomics of Intralocus Sexual Conflict: Gene Expression Patterns in Females Change in Response to Selection on a Male Secondary Sexual Trait in the Bulb Mite

Genome Biol Evol
PMCID: 5010903
PMID: 27401174
DOI: 10.1093/gbe/evw169

[…] Blast2GO (Version 3.0) (), where mapping and functional annotation were done using default settings. Enrichment analyses were performed in R (Version 3.2.3) () using Bioconductor packages GOstats (), GSEABase (), and ( For the genes differentially expressed in the F-line […]


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