netDx
This is the released version of netDx; for the devel version, see netDx.
Network-based patient classifier
Bioconductor version: Release (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 utoronto.ca>
citation("netDx")):
Installation
To install this package, start R (version "4.4") 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
| Reference Manual |
Details
| biocViews | BiomedicalInformatics, Classification, Network, Software, SystemsBiology |
| Version | 1.18.0 |
| 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 |
See More
| Suggests | curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3, clusterExperiment, netSmooth, scater |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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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 |