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This is the development version of netDx; for the stable release version, see netDx.

Network-based patient classifier

Bioconductor version: Development (3.20)

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>

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


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if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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01. Build & test classifier with clinical and multi-omic data & pathway features HTML R Script
Reference Manual PDF


biocViews BiomedicalInformatics, Classification, Network, Software, SystemsBiology
Version 1.17.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
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Suggests curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3, clusterExperiment, netSmooth, scater
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Source Package netDx_1.17.0.tar.gz
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