netDx

DOI: 10.18129/B9.bioc.netDx    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see netDx.

Network-based patient classifier

Bioconductor version: 3.11

netDx is a general-purpose algorithm to build a patient classifier from heterogenous patient data. The method converts data into patient similarity networks at the level of features. Feature selection identifies features of predictive value to each class. Methods are provided for versatile predictor design and performance evaluation using standard measures. netDx natively groups molecular data into pathway-level features and connects with Cytoscape for network visualization of pathway themes. For method details see: Pai et al. (2019). netDx: interpretable patient classification using integrated patient similarity networks. Molecular Systems Biology. 15, e8497

Author: Shraddha Pai [aut, cre] , Philipp Weber [aut], Ahmad Shah [aut], Luca Giudice [aut], Shirley Hui [aut], Ruth Isserlin [aut], Luca Giudice [aut], Hussam Kaka [aut], Gary Bader [aut]

Maintainer: Shraddha Pai <shraddha.pai at utoronto.ca>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("netDx")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("netDx")

 

HTML	R Script	01. Build binary predictor and view performance, top features and integrated Patient Similarity Network
HTML	R Script	02. Build three-way classifier (N-way; N>2) from multi-omic data
HTML	R Script	03. Build classifier from sparse genetic data
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiomedicalInformatics, Classification, Network, Software, SystemsBiology
Version	1.0.4
In Bioconductor since	BioC 3.11 (R-4.0) (0.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	ROCR, pracma, ggplot2, RCy3, glmnet, igraph, reshape2, parallel, stats, utils, MultiAssayExperiment, graphics, grDevices, methods, BiocFileCache, GenomicRanges, bigmemory, doParallel, foreach, combinat, rappdirs, GenomeInfoDb, S4Vectors, IRanges, RColorBrewer, scater, netSmooth, clusterExperiment, Rtsne
LinkingTo
Suggests	curatedTCGAData, TCGAutils, rmarkdown, testthat, knitr
SystemRequirements
Enhances
URL	http://netdx.org
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	netDx_1.0.4.tar.gz
Windows Binary	netDx_1.0.3.zip
macOS 10.13 (High Sierra)	netDx_0.99.18.tgz
Source Repository	git clone https://git.bioconductor.org/packages/netDx
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/netDx
Package Short Url	https://bioconductor.org/packages/netDx/
Package Downloads Report	Download Stats