PGSEA
(Package: PGSEA) :
Parametric Gene Set Enrichment Analysis
This package contains functions for an exploratory parametric analysis of gene expression data. This type of analysis can assist in determining of lists of genes, such as those deregulated in defined experimental systems, are similarly deregulated in other data sets.
● Data Source:
BioConductor
● Keywords: htest
● Alias: PGSEA
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convertSmc
(Package: PGSEA) :
Convert Entrez ID based "smc" object
This function will convert the Entrez IDs of an smc object to the corresponding Entrez IDs from a different species. Data from the homologene project is downloaded and used within this function.
● Data Source:
BioConductor
● Keywords: manip
● Alias: convertSmc
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editSmc
(Package: PGSEA) :
Edit "smc" objects
This function will edit a single or list of "smc" objects.
● Data Source:
BioConductor
● Keywords: manip
● Alias: editSmc
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go2smc
(Package: PGSEA) :
Gene Ontology 2 "smc"
This function creates "smc" objects from the "GO" Bioconductor library.
● Data Source:
BioConductor
● Keywords: manip
● Alias: go2smc
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kegg2smc
(Package: PGSEA) :
KEGG pathway to "smc"
This function creates "smc" objects from the "KEGG" Bioconductor library.
● Data Source:
BioConductor
● Keywords: manip
● Alias: kegg2smc
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This function will read a "gmt" file into R, returning results as a list of SMC objects.
● Data Source:
BioConductor
● Keywords: data
● Alias: readGmt
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readSmc
(Package: PGSEA) :
Read SMC files
This function reads in SMCs (simple molecular concepts) from individual text files.
● Data Source:
BioConductor
● Keywords: data
● Alias: readSmc, smc-class
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scanSmc
(Package: PGSEA) :
Scan through smc objects
This function scans through smc objects and returns those with specified attributes.
● Data Source:
BioConductor
● Keywords: manip
● Alias: scanSmc
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smcPlot
(Package: PGSEA) :
Plot PGSEA results
This basic function will plot results from PGSEA with easy altering of margins, colors, and text.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: smcPlot
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This function writes out SMC objects into .gmt file format
● Data Source:
BioConductor
● Keywords: data
● Alias: writeGmt
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