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netDx

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

Network-based patient classifier


Bioconductor version: Development (3.19)

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 utoronto.ca>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews BiomedicalInformatics, Classification, Network, Software, SystemsBiology
Version 1.15.0
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
System Requirements
URL http://netdx.org
See More
Suggests curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3, clusterExperiment, netSmooth, scater
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package netDx_1.15.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/netDx
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/netDx
Bioc Package Browser https://code.bioconductor.org/browse/netDx/
Package Short Url https://bioconductor.org/packages/netDx/
Package Downloads Report Download Stats