SPIA: Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Version 2.28.0

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>
Bioconductor views GraphAndNetwork Microarray
Date of publicationNone
MaintainerAdi Laurentiu Tarca <atarca@med.wayne.edu>
Licensefile LICENSE
Version2.28.0
URL http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SPIA")

Popular 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...
See all...

All man pages Function index File listing

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...

Functions

ALL_Colorectal Man page
ALL_Vessels Man page
DE_Colorectal Man page
DE_Vessels Man page
Vessels Man page
colorectalcancer Man page
combfunc Man page Source code
getP2 Man page Source code
makeSPIAdata Man page Source code
plotP Man page Source code
spia Man page Source code
top Man page

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
SPIA documentation built on May 20, 2017, 10:28 p.m.

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

Please suggest features or report bugs in the GitHub issue tracker.

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