DOI: 10.18129/B9.bioc.netDx  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see netDx.

Network-based patient classifier

Bioconductor version: 3.16

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], Anne Nøhr [ctb], Indy Ng [ctb], Ruth Isserlin [aut], Hussam Kaka [aut], Gary Bader [aut]

Maintainer: Shraddha Pai <shraddha.pai at>

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HTML R Script 01. Build & test classifier with clinical and multi-omic data & pathway features
HTML R Script 02. Running netDx with data in table format
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biocViews BiomedicalInformatics, Classification, Network, Software, SystemsBiology
Version 1.9.0
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports ROCR, pracma, ggplot2, glmnet, igraph, reshape2, parallel, stats, utils, MultiAssayExperiment, graphics, grDevices, methods, BiocFileCache, GenomicRanges, bigmemory, doParallel, foreach, combinat, rappdirs, GenomeInfoDb, S4Vectors, IRanges, RColorBrewer, Rtsne, httr, plotrix
Suggests curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3, clusterExperiment, netSmooth, scater
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