EGSEA-package
(Package: EGSEA) :
Ensemble of Gene Enrichment Analysis (EGSEA)
This packages provides the implementatino of the EGSEA algorithm and addition functions to help perform GSE analysis
● Data Source:
BioConductor
● Keywords:
● Alias: EGSEA, EGSEA-package
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buildCustomIdxEZID
(Package: EGSEA) :
Custom Gene Set Collection Index
It creates gene set collections from a given list of gene sets to be used for the EGSEA analysis.
● Data Source:
BioConductor
● Keywords:
● Alias: buildCustomIdxEZID
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buildGeneSetDBIdxEZID
(Package: EGSEA) :
Gene Set Collection Indexes from the GeneSetDB Database
It prepares the GeneSetDB gene set collections to be used for the EGSEA analysis.
● Data Source:
BioConductor
● Keywords:
● Alias: buildGeneSetDBIdxEZID
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buildIdxEZID
(Package: EGSEA) :
Generate Gene Set Collection Indexes from the MSigDB and KEGG
It prepares the MSigDB and KEGG gene set collections to be used for the EGSEA analysis.
● Data Source:
BioConductor
● Keywords:
● Alias: buildIdxEZID
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buildKEGGIdxEZID
(Package: EGSEA) :
Gene Set Collection Index from the KEGG Database
It prepares the KEGG pathway collection to be used for the EGSEA analysis.
● Data Source:
BioConductor
● Keywords:
● Alias: buildKEGGIdxEZID
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buildMSigDBIdxEZID
(Package: EGSEA) :
Gene Set Collection Indexes from the MSigDB Database
It prepares the MSigDB gene set collections to be used for the EGSEA analysis.
● Data Source:
BioConductor
● Keywords:
● Alias: buildMSigDBIdxEZID
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egsea
(Package: EGSEA) :
Ensemble of Gene Set Enrichment Analyses Function
This is the main function to carry out gene set enrichment analysis using the EGSEA algorithm. This function is aimed to extend the limma-voom pipeline of RNA-seq analysis.
● Data Source:
BioConductor
● Keywords:
● Alias: egsea
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egsea.base
(Package: EGSEA) :
EGSEA Base GSE Methods
It lists the supported GSEA methods
● Data Source:
BioConductor
● Keywords:
● Alias: egsea.base
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egsea.cnt
(Package: EGSEA) :
Ensemble of Gene Set Enrichment Analyses Function
This is the main function to carry out gene set enrichment analysis using the EGSEA algorithm. This function is aimed to use the raw count matrix to perform the EGSEA analysis.
● Data Source:
BioConductor
● Keywords:
● Alias: egsea.cnt
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egsea.combine
(Package: EGSEA) :
EGSEA P-value Combining Options
It lists the p-value combining methods
● Data Source:
BioConductor
● Keywords:
● Alias: egsea.combine
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