Subnetwork Integration for Multi-Modal Signatures

Algorithms to create prognostic biomarkers using biological genesets or networks.



  • predictive models (logistic regression)

SIMMS 1.2.0


  • support data scaling beyond z-scores including median and custom centering for methylation data.
  • general improvement to documentation
  • improved vignettes explaining how to structure custom network DB and annotation data
  • added censorship tick marks for KM curves

SIMMS 1.1.2


  • Updates to handling of betas for discrete/nominal variables akin to predict()
  • Formalised terminology for copy-number aberrations as 'cna' instead of 'cnv'
  • Improved interaction model (abs(beta)) such that higher scores are given to same signed (two) genes. Also fixed the extraction of beta/P from correct interaction row when >2 levels discrete/nominal variables are specified
  • Implemented inline documentation using Roxygen

SIMMS 1.1.1


  • Converted elastic-net mixing parameter alpha [0,1] to search for optimal alpha
  • Implemented parallel processing for glm alpha search space

SIMMS 1.1.0


  • Added elastic-net mixing parameter to support alpha [0,1] i.e ridge to LASSO

SIMMS 1.0.3


  • Added rmarkdown in Suggests section

SIMMS 1.0.2


  • Exception handling for interaction model
  • Save selected features for every subnet that pass p.threshold and used in estimating subnet MDS
  • Fixed NAMESPACE to comply with latest CRAN policies of explicit exports/imports

SIMMS 1.0.1


  • Fixed vignettes to comply with CRAN policy of not writing to user's home directory

SIMMS 1.0.0


  • Added Generalised Linear Models (L1-penalty) based Cox models for fitting multi-subnetwork models

  • Added vignettes

  • Added full support for discrete data types e.g copy-number aberrations

  • General run-time optimisations and exception handling

  • Added additional network databases including TCGA MEMo subnetworks for breast, colon, glioblastoma, kidney and ovarian cancers

SIMMS 0.0.1


  • Added SIMMS first implementation

Reference manual

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1.3.1 by Syed Haider, a year ago

Browse source code at

Authors: Syed Haider [aut, cre] , Paul C. Boutros [aut] , Michal Grzadkowski [ctb]

Documentation:   PDF Manual  

GPL-2 license

Imports randomForestSRC

Depends on survival, MASS, glmnet, doParallel, foreach

Suggests knitr, rmarkdown, xtable

See at CRAN