SPIA: 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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SPIA")
AuthorAdi Laurentiu Tarca <atarca@med.wayne.edu>, Purvesh Kathri <purvesh@cs.wayne.edu> and Sorin Draghici <sorin@wayne.edu>
Bioconductor views GraphAndNetwork Microarray
Date of publicationNone
MaintainerAdi Laurentiu Tarca <atarca@med.wayne.edu>
Licensefile LICENSE
Version2.26.0
http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1

View on Bioconductor

Files

COPYING
DESCRIPTION
LICENSE
NAMESPACE
R
R/combfunc.R R/getP2.R R/makeSPIAdata.R R/plotP.R R/spia.R
build
build/vignette.rds
data
data/Vessels.RData
data/colorectalcancer.RData
inst
inst/doc
inst/doc/SPIA.R
inst/doc/SPIA.Rnw
inst/doc/SPIA.pdf
inst/extdata
inst/extdata/hsaSPIA.RData
inst/extdata/keggxml
inst/extdata/keggxml/hsa
inst/extdata/keggxml/hsa/hsa03013.xml
inst/extdata/keggxml/hsa/hsa03050.xml
inst/extdata/keggxml/hsa/hsa04914.xml
inst/extdata/keggxml/hsa/hsa05210.xml
inst/extdata/mmuSPIA.RData
man
man/SPIA-internal.Rd man/Vessels.Rd man/colorectalcancer.Rd man/combfunc.Rd man/makeSPIAdata.Rd man/plotP.Rd man/spia.Rd
vignettes
vignettes/PFs.png
vignettes/SPIA.Rnw
vignettes/SPIA.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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