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.

AuthorAdi Laurentiu Tarca <atarca@med.wayne.edu>, Purvesh Kathri <purvesh@cs.wayne.edu> and Sorin Draghici <sorin@wayne.edu>
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

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

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

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