Package: netprioR 1.38.0

Fabian Schmich

netprioR: A model for network-based prioritisation of genes

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.

Authors:Fabian Schmich

netprioR_1.38.0.tar.gz
netprioR_1.38.0.zip(r-4.7-any)netprioR_1.38.0.zip(r-4.6-any)netprioR_1.38.0.zip(r-4.5-any)
netprioR_1.38.0.tgz(r-4.6-any)netprioR_1.38.0.tgz(r-4.5-any)
netprioR_1.38.0.tar.gz(r-4.7-any)netprioR_1.38.0.tar.gz(r-4.6-any)
netprioR_1.38.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
netprioR/json (API)

# Install 'netprioR' in R:

install.packages('netprioR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

simulation - Example data: Simulated networks, phenotypes and labels for N = 1000 genes

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology cellbasedassays preprocessing network

2.18 score 1 scripts 9 exports 35 dependencies

Last updated from:b0c1c54368 (on RELEASE_3_23). Checks:9 ERROR, 1 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	151
linux-devel-x86_64	ERROR	228
source / vignettes	ERROR	207
linux-release-x86_64	ERROR	164
macos-release-arm64	ERROR	126
macos-oldrel-arm64	ERROR	91
windows-devel	ERROR	119
windows-release	ERROR	117
windows-oldrel	ERROR	110
wasm-release	OK	143

Exports:fit netprioR ranks ROC simulate_labels simulate_network_random simulate_network_scalefree simulate_phenotype weights

Dependencies:cli codetools cpp11 doParallel dplyr farver foreach generics ggplot2 glue gridExtra gtable isoband iterators labeling lattice lifecycle magrittr Matrix pillar pkgconfig pROC R6 RColorBrewer Rcpp rlang S7 scales sparseMVN tibble tidyselect utf8 vctrs viridisLite withr

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Package: netprioR	netprioR-package
bandwidth	bandwidth
Class Mass Normalization (CMN) from Zhu et al., 2003	cmn
Conjugate Gradient Solver	conjugate_gradient
Cuthill McKee (CM) algorithm	cuthill_mckee
Fit 'netprioR' model	fit fit,netprioR-method
Graph Laplacian	laplacian
Fit netprioR model	learn
netprioR	netprioR netprioR,list,matrix,factor-method netprioR-class
Normalise kernel	norm_kern
Plot method for 'netprioR' objects	plot.netprioR
Retrieve ranked prioritisation list	ranks ranks,netprioR-method
Compute ROC curve from netprioR model and true labels	ROC ROC,netprioR-method
Simulate labels	simulate_labels
Simulate random networks with predefined number of members for each of the two groups and the number of neighbours for each node	simulate_network_random
Simulate scalefree networks	simulate_network_scalefree
Simulate phenotypes correlated to labels pivoted into two groups	simulate_phenotype
Example data: Simulated networks, phenotypes and labels for N = 1000 genes	simulation
Retrieve network weights	weights weights,netprioR-method