Package: netDx
Title: Network-based patient classifier
Version: 1.14.0
Authors@R: c(person("Shraddha", "Pai", 
		email = "shraddha.pai@utoronto.ca", 
		role = c("aut", "cre"),
	  comment = c(ORCID = "0000-0002-1048-581X")), 
	person("Philipp","Weber",role="aut"),
	person("Ahmad","Shah", role="aut"),
	person("Luca","Giudice",role="aut"),
	person("Shirley","Hui",role="aut"),
	person("Anne","Nøhr",role="ctb"),
	person("Indy","Ng",role="ctb"),
	person("Ruth","Isserlin",role="aut"),
	person("Hussam","Kaka", role="aut"),
	person("Gary","Bader",role="aut"))
Description: 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
Depends: R (>= 3.6)
Suggests: curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3,
        clusterExperiment, netSmooth, scater
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
VignetteBuilder: knitr
Encoding: UTF-8
License: MIT + file LICENSE
LazyData: false
URL: http://netdx.org
biocViews: Classification, BiomedicalInformatics, Network,
        SystemsBiology
RoxygenNote: 7.1.2
git_url: https://git.bioconductor.org/packages/netDx
git_branch: RELEASE_3_18
git_last_commit: 6e24937
git_last_commit_date: 2023-10-24
Date/Publication: 2023-10-26
NeedsCompilation: no
Packaged: 2023-10-27 08:13:38 UTC; biocbuild
Author: Shraddha Pai [aut, cre] (<https://orcid.org/0000-0002-1048-581X>),
  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@utoronto.ca>
Built: R 4.3.1; ; 2023-10-28 19:03:31 UTC; unix
