Package: netprioR 1.33.0

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_1.33.0.tar.gz
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netprioR.pdf |netprioR.html✨
netprioR/json (API)
NEWS

# Install 'netprioR' in R:

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

Datasets:

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

On BioConductor:netprioR-1.33.0(bioc 3.21)netprioR-1.32.0(bioc 3.20)

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

immunooncology cellbasedassays preprocessing network

4.00 score 1 scripts 152 downloads 9 exports 40 dependencies

Last updated 2 months agofrom:9afdf839ef. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 10 2024
R-4.5-win	OK	Dec 10 2024
R-4.5-linux	OK	Dec 10 2024
R-4.4-win	OK	Dec 10 2024
R-4.4-mac	OK	Dec 10 2024
R-4.3-win	OK	Dec 10 2024
R-4.3-mac	OK	Dec 10 2024

Exports:fit netprioR ranks ROC simulate_labels simulate_network_random simulate_network_scalefree simulate_phenotype weights

Dependencies:cli codetools colorspace doParallel dplyr fansi farver foreach generics ggplot2 glue gridExtra gtable isoband iterators labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig plyr pROC R6 RColorBrewer Rcpp rlang scales sparseMVN tibble tidyselect utf8 vctrs viridisLite withr

netprioR Vignette

Fabian Schmich

Rendered fromnetprioR.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2016-05-26
Started: 2016-05-26

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