netprioR: A model for network-based prioritisation of genes

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A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts.

Author
Fabian Schmich
Date of publication
None
Maintainer
Fabian Schmich <fabian.schmich@bsse.ethz.ch>
License
GPL-3
Version
1.0.0
URLs

View on Bioconductor

Man pages

bandwidth
bandwidth
cmn
Class Mass Normalization (CMN) from Zhu et al., 2003
conjugate_gradient
Conjugate Gradient Solver
cuthill_mckee
Cuthill McKee (CM) algorithm
fit-methods
Fit 'netprioR' model
laplacian
Graph Laplacian
learn
Fit netprioR model
netprioR-class
netprioR
netprioR-package
Package: netprioR
norm_kern
Normalise kernel
plot.netprioR
Plot method for 'netprioR' objects
ranks-methods
Retrieve ranked prioritisation list
ROC-methods
Compute ROC curve from netprioR model and true labels
simulate_labels
Simulate labels
simulate_network_random
Simulate random networks with predefined number of members...
simulate_network_scalefree
Simulate scalefree networks
simulate_phenotype
Simulate phenotypes correlated to labels pivoted into two...
simulation
Example data: Simulated networks, phenotypes and labels for N...
weights-methods
Retrieve network weights

Files in this package

netprioR/DESCRIPTION
netprioR/NAMESPACE
netprioR/R
netprioR/R/netprioR-class.R
netprioR/R/netprioR-functions.R
netprioR/R/netprioR-generics.R
netprioR/R/netprioR-methods.R
netprioR/R/netprioR-package.R
netprioR/R/netprioR-simulation.R
netprioR/README.md
netprioR/build
netprioR/build/vignette.rds
netprioR/data
netprioR/data/simulation.rdata
netprioR/inst
netprioR/inst/NEWS
netprioR/inst/doc
netprioR/inst/doc/netprioR.R
netprioR/inst/doc/netprioR.Rmd
netprioR/inst/doc/netprioR.html
netprioR/inst/example
netprioR/inst/example/data_simulation.R
netprioR/man
netprioR/man/ROC-methods.Rd
netprioR/man/bandwidth.Rd
netprioR/man/cmn.Rd
netprioR/man/conjugate_gradient.Rd
netprioR/man/cuthill_mckee.Rd
netprioR/man/fit-methods.Rd
netprioR/man/laplacian.Rd
netprioR/man/learn.Rd
netprioR/man/netprioR-class.Rd
netprioR/man/netprioR-package.Rd
netprioR/man/norm_kern.Rd
netprioR/man/plot.netprioR.Rd
netprioR/man/ranks-methods.Rd
netprioR/man/simulate_labels.Rd
netprioR/man/simulate_network_random.Rd
netprioR/man/simulate_network_scalefree.Rd
netprioR/man/simulate_phenotype.Rd
netprioR/man/simulation.Rd
netprioR/man/weights-methods.Rd
netprioR/vignettes
netprioR/vignettes/netprioR.Rmd