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cff-version: 1.2.0
message: 'To cite package "metasnf" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'metasnf: Meta Clustering with Similarity Network Fusion'
version: 1.1.2
doi: 10.32614/CRAN.package.metasnf
identifiers:
- type: url
  value: https://github.com/BRANCHlab/metasnf/
abstract: Framework to facilitate patient subtyping with similarity network fusion
  and meta clustering. The similarity network fusion (SNF) algorithm was introduced
  by Wang et al. (2014) in <https://doi.org/10.1038/nmeth.2810>. SNF is a data integration
  approach that can transform high-dimensional and diverse data types into a single
  similarity network suitable for clustering with minimal loss of information from
  each initial data source. The meta clustering approach was introduced by Caruana
  et al. (2006) in <https://doi.org/10.1109/ICDM.2006.103>. Meta clustering involves
  generating a wide range of cluster solutions by adjusting clustering hyperparameters,
  then clustering the solutions themselves into a manageable number of qualitatively
  similar solutions, and finally characterizing representative solutions to find ones
  that are best for the user's specific context. This package provides a framework
  to easily transform multi-modal data into a wide range of similarity network fusion-derived
  cluster solutions as well as to visualize, characterize, and validate those solutions.
  Core package functionality includes easy customization of distance metrics, clustering
  algorithms, and SNF hyperparameters to generate diverse clustering solutions; calculation
  and plotting of associations between features, between patients, and between cluster
  solutions; and standard cluster validation approaches including resampled measures
  of cluster stability, standard metrics of cluster quality, and label propagation
  to evaluate generalizability in unseen data. Associated vignettes guide the user
  through using the package to identify patient subtypes while adhering to best practices
  for unsupervised learning.
authors:
- family-names: Velayudhan
  given-names: Prashanth S
  email: psvelayu@gmail.com
- family-names: Xu
  given-names: Xiaoqiao
- family-names: Kallurkar
  given-names: Prajkta
- family-names: Balbon
  given-names: Ana Patricia
- family-names: Secara
  given-names: Maria T
- family-names: Taback
  given-names: Adam
- family-names: Sabac
  given-names: Denise
- family-names: Chan
  given-names: Nicholas
- family-names: Ma
  given-names: Shihao
- family-names: Wang
  given-names: Bo
- family-names: Felsky
  given-names: Daniel
- family-names: Ameis
  given-names: Stephanie H
- family-names: Cox
  given-names: Brian
- family-names: Hawco
  given-names: Colin
- family-names: Erdman
  given-names: Lauren
- family-names: Wheeler
  given-names: Anne L
  email: anne.wheeler@sickkids.ca
repository: https://branchlab.r-universe.dev
repository-code: https://github.com/BRANCHlab/metasnf
commit: fc11443ec29058206996cbc2dfe232b698d1d6bd
url: https://branchlab.github.io/metasnf/
contact:
- family-names: Velayudhan
  given-names: Prashanth S
  email: psvelayu@gmail.com