SPIA v2.24.0

Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations

This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.

Functions in SPIA

Name Description
combfunc Combining two p-values using Fisher's product or normal inversion method
plotP SPIA two-way evidence plot
SPIA-internal Internal SPIA functions
colorectalcancer Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.
makeSPIAdata Process KGML files for spia analysis
Vessels Results from a microarray expriment comparing umbilical veins and arteries tissues
spia Signaling Pathway Impact Analysis (SPIA) based on over-representation and signaling perturbations accumulation
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Details

Date 2013-2-20
License file LICENSE
License_restricts_use yes
URL http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1
Collate spia.R plotP.R combfunc.R getP2.R makeSPIAdata.R
LazyLoad yes
Packaged 2011-11-01 17:54:41 UTC; biocbuild
biocViews Microarray, GraphAndNetwork

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