netDx
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see netDx.
Network-based patient classifier
Bioconductor version: 3.11
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], Luca Giudice [aut], Hussam Kaka [aut], Gary Bader [aut]
Maintainer: Shraddha Pai <shraddha.pai at utoronto.ca>
citation("netDx")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("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")| 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 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, Classification, Network, Software, SystemsBiology |
| Version | 1.0.4 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 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 |
| System Requirements | |
| URL | http://netdx.org |
See More
| Suggests | curatedTCGAData, TCGAutils, rmarkdown, testthat, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | netDx_1.0.4.tar.gz |
| Windows Binary | netDx_1.0.3.zip |
| macOS 10.13 (High Sierra) | netDx_0.99.18.tgz |
| 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 |
| Old Source Packages for BioC 3.11 | Source Archive |