PANR: Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.

AuthorXin Wang <xin_wang@hms.harvard.edu>
Date of publicationNone
MaintainerXin Wang <xin_wang@hms.harvard.edu>
LicenseArtistic-2.0
Version1.20.0

View on Bioconductor

Functions

assoScore Man page
Bakal2007 Man page
Bakal2007Cluster Man page
BetaMixture Man page
BetaMixture-class Man page
bm1 Man page
buildPAN Man page
buildPAN,PAN,character_Or_missing,list_Or_missing,logical_Or_mis Man page
cosineDist Man page
cosineSim Man page
edgeWeight Man page
edgeWeight, PAN-method Man page
exportPAN Man page
exportPAN,PAN,character_Or_missing,character_Or_missing,numeric_ Man page
fitBM Man page
fitBM,BetaMixture,list_Or_missing,list_Or_missing,logical_Or_mis Man page
fitNULL Man page
fitNULL,BetaMixture,numeric_Or_integer_Or_missing,numeric_Or_int Man page
infer Man page
infer,PAN,list,logical_Or_missing,logical_Or_missing-method Man page
nodeColor Man page
p2SNR Man page
p2SNR,BetaMixture,numeric_Or_integer-method Man page
PAN Man page
PAN-class Man page
permNULL Man page
permNULL,BetaMixture,character_Or_missing-method Man page
pvclustModule Man page
pvclustModule,PAN,numeric_Or_integer_Or_missing,character_Or_mis Man page
sigModules Man page
sigModules,PAN,numeric_Or_integer_Or_missing,numeric_Or_integer_ Man page
SNR2p Man page
SNR2p,BetaMixture,numeric_Or_integer-method Man page
summarize Man page
summarize,BetaMixture,character_Or_missing-method Man page
summarize,PAN,character_Or_missing-method Man page
view Man page
view,BetaMixture,character_Or_missing-method Man page
viewLegend Man page
viewLegend,PAN,character_Or_missing-method Man page
viewNestedModules Man page
viewNestedModules,PAN,numeric_Or_integer_Or_missing,numeric_Or_i Man page
viewPAN Man page
viewPAN,PAN,character_Or_missing,numeric_Or_integer_Or_missing,c Man page

Files

PANR/DESCRIPTION
PANR/NAMESPACE
PANR/R
PANR/R/AllClasses.R PANR/R/AllGenerics.R PANR/R/BetaMixture-methods.R PANR/R/PAN-methods.R PANR/R/assoScore.R PANR/R/classUnions.R PANR/R/panGraphics.R
PANR/build
PANR/build/vignette.rds
PANR/data
PANR/data/Bakal2007.RData
PANR/data/Bakal2007Cluster.RData
PANR/data/bm.RData
PANR/data/datalist
PANR/inst
PANR/inst/CHANGES
PANR/inst/NEWS
PANR/inst/doc
PANR/inst/doc/PANR-Vignette.R
PANR/inst/doc/PANR-Vignette.Rnw
PANR/inst/doc/PANR-Vignette.pdf
PANR/man
PANR/man/BetaMixture-class.Rd PANR/man/PAN-class.Rd PANR/man/SNR2p.Rd PANR/man/assoScore.Rd PANR/man/buildPAN.Rd PANR/man/cosineSim.Rd PANR/man/data-Bakal2007.Rd PANR/man/edgeWeight.Rd PANR/man/exportPAN.Rd PANR/man/fitBM.Rd PANR/man/fitNULL.Rd PANR/man/infer.Rd PANR/man/p2SNR.Rd PANR/man/permNULL.Rd PANR/man/pvclustModule.Rd PANR/man/sigModules.Rd PANR/man/summarize.Rd PANR/man/view.Rd PANR/man/viewLegend.Rd PANR/man/viewNestedModules.Rd PANR/man/viewPAN.Rd
PANR/vignettes
PANR/vignettes/PANR-Vignette.Rnw
PANR/vignettes/fullPAN.pdf
PANR/vignettes/overview.png
PANR/vignettes/pvmodule.pdf
PANR/vignettes/sigmod.pdf

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

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

All documentation is copyright its authors; we didn't write any of that.