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.

Author
Adi Laurentiu Tarca <atarca@med.wayne.edu>, Purvesh Kathri <purvesh@cs.wayne.edu> and Sorin Draghici <sorin@wayne.edu>
Date of publication
None
Maintainer
Adi Laurentiu Tarca <atarca@med.wayne.edu>
License
file LICENSE
Version
2.26.0
URLs

View on Bioconductor

Man pages

colorectalcancer
Results from a microarray experiment comparing colorectal...
combfunc
Combining two p-values using Fisher's product or normal...
makeSPIAdata
Process KGML files for spia analysis
plotP
SPIA two-way evidence plot
spia
Signaling Pathway Impact Analysis (SPIA) based on...
SPIA-internal
Internal SPIA functions
Vessels
Results from a microarray expriment comparing umbilical veins...

Files in this package

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