netDx

DOI: 10.18129/B9.bioc.netDx    

Network-based patient classifier

Bioconductor version: Release (3.12)

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], Hussam Kaka [aut], Gary Bader [aut]

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

Citation (from within R, enter citation("netDx")):

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 1.2.0
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_1.2.0.tar.gz
Windows Binary netDx_1.1.4.zip
macOS 10.13 (High Sierra)
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

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