netDx

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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

Network-based patient classifier

Bioconductor version: Development (3.21)

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] (ORCID: ), 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 "4.5") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, Classification, Network, Software, SystemsBiology
Version	1.19.1
In Bioconductor since	BioC 3.11 (R-4.0) (4.5 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

Suggests	curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3, clusterExperiment, netSmooth, scater
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/netDx/
Package Downloads Report	Download Stats