SIMMS: Subnetwork Integration for Multi-Modal Signatures

Algorithms to create prognostic biomarkers using biological networks.

AuthorSyed Haider, Michal Grzadkowski, Paul C. Boutros
Date of publication2015-09-21 17:57:55
MaintainerSyed Haider <Syed.Haider@oicr.on.ca>
LicenseGPL-2
Version1.0.2

View on CRAN

Man pages

calculate.meta.survival: Fit a meta-analytic Cox proportional hazards model to a...

calculate.network.coefficients: Calculate Cox statistics for input dataset

calculate.sensitivity.stats: Computes sensitivity measures

create.classifier.multivariate: Trains and tests a multivariate survival model

create.classifier.univariate: Trains and tests a univariate (per subnetwork module)...

create.KM.plot: Plots Kaplan-meier survival curve for a given risk grouping &...

create.sensitivity.plot: Plots sensitivity analysis for class label dichotomization at...

create.survivalplots: Plots Kaplan-meier survival curves

create.survobj: Utility function for loading meta-analysis lists

derive.network.features: Derive univariate features from pathway-derived networks

dichotomize.dataset: Dichotomize a single dataset

dichotomize.meta.dataset: Dichotomize and unlist a meta-analysis list

fit.coxmodel: Fit a Cox proportional hazards model

fit.interaction.model: Cox model two features separately and together

fit.survivalmodel: Trains a multivariate survival model

get.adjacency.matrix: A utility function to convert tab delimited networks file...

get.chisq.stats: Applies survdiff function

get.program.defaults: A utility function to return the inst/ directory of the...

load.cancer.datasets: Load all cancer meta-analysis datasets

make.matrix: Utility function used by 'get.adjacency.matrix()'

pred.survivalmodel: Apply a multivariate survival model to validation datasets

prepare.training.validation.datasets: Prepare training and validation datasets

SIMMS: SIMMS - Subnetwork Integration for Multi-Modal Signatures

Files in this package

SIMMS
SIMMS/inst
SIMMS/inst/programdata
SIMMS/inst/programdata/networkdb
SIMMS/inst/programdata/networkdb/MEMo.BRCA
SIMMS/inst/programdata/networkdb/MEMo.BRCA/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/MEMo.BRCA/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/MEMo.BRCA/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/networkdb/Mammaprint
SIMMS/inst/programdata/networkdb/Mammaprint/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/Mammaprint/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/Mammaprint/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/networkdb/Oncotypedx
SIMMS/inst/programdata/networkdb/Oncotypedx/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/Oncotypedx/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/Oncotypedx/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/networkdb/PI3K
SIMMS/inst/programdata/networkdb/PI3K/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/PI3K/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/PI3K/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/networkdb/MEMo
SIMMS/inst/programdata/networkdb/MEMo/HGNC_Entrez_map.txt
SIMMS/inst/programdata/networkdb/MEMo/pathway_based_sub_networks__HGNC.txt
SIMMS/inst/programdata/networkdb/MEMo/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/MEMo/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/MEMo/map.hgnc.entrez.R
SIMMS/inst/programdata/networkdb/MEMo/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/networkdb/HiC.gm06690
SIMMS/inst/programdata/networkdb/HiC.gm06690/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/HiC.gm06690/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/HiC.gm06690/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/networkdb/MEMo.GBM
SIMMS/inst/programdata/networkdb/MEMo.GBM/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/MEMo.GBM/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/MEMo.GBM/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/networkdb/default
SIMMS/inst/programdata/networkdb/default/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/default/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/default/pathway_based_networks.txt
SIMMS/inst/programdata/networkdb/default/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/networkdb/test
SIMMS/inst/programdata/networkdb/test/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/test/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/test/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/networkdb/MEMo.KIRC
SIMMS/inst/programdata/networkdb/MEMo.KIRC/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/MEMo.KIRC/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/MEMo.KIRC/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/networkdb/MEMo.OV
SIMMS/inst/programdata/networkdb/MEMo.OV/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/MEMo.OV/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/MEMo.OV/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/networkdb/MEMo.COADREAD
SIMMS/inst/programdata/networkdb/MEMo.COADREAD/pathway_based_sub_networks.txt
SIMMS/inst/programdata/networkdb/MEMo.COADREAD/pathway_based_sub_networks_all.txt
SIMMS/inst/programdata/networkdb/MEMo.COADREAD/pathway_based_networks_flattened.txt
SIMMS/inst/programdata/testdata
SIMMS/inst/programdata/testdata/datasets.txt
SIMMS/inst/programdata/testdata/Breastdata1
SIMMS/inst/programdata/testdata/Breastdata1/patient_annotation.txt
SIMMS/inst/programdata/testdata/Breastdata1/mRNA_abundance.txt
SIMMS/inst/programdata/testdata/Breastdata2
SIMMS/inst/programdata/testdata/Breastdata2/patient_annotation.txt
SIMMS/inst/programdata/testdata/Breastdata2/mRNA_abundance.txt
SIMMS/inst/doc
SIMMS/inst/doc/Using-SIMMS.R
SIMMS/inst/doc/Using-SIMMS.html
SIMMS/inst/doc/Using-SIMMS.Rmd
SIMMS/NAMESPACE
SIMMS/NEWS
SIMMS/R
SIMMS/R/get.chisq.stats.R SIMMS/R/get.program.defaults.R SIMMS/R/create.KM.plot.R SIMMS/R/calculate.meta.survival.R SIMMS/R/fit.survivalmodel.R SIMMS/R/calculate.sensitivity.stats.R SIMMS/R/make.matrix.R SIMMS/R/fit.interaction.model.R SIMMS/R/calculate.network.coefficients.R SIMMS/R/fit.coxmodel.R SIMMS/R/load.cancer.datasets.R SIMMS/R/dichotomize.dataset.R SIMMS/R/get.adjacency.matrix.R SIMMS/R/derive.network.features.R SIMMS/R/create.survobj.R SIMMS/R/dichotomize.meta.dataset.R SIMMS/R/create.sensitivity.plot.R SIMMS/R/create.classifier.multivariate.R SIMMS/R/pred.survivalmodel.R SIMMS/R/prepare.training.validation.datasets.R SIMMS/R/create.survivalplots.R SIMMS/R/create.classifier.univariate.R
SIMMS/vignettes
SIMMS/vignettes/GitHub2.css
SIMMS/vignettes/Using-SIMMS.Rmd
SIMMS/MD5
SIMMS/build
SIMMS/build/vignette.rds
SIMMS/DESCRIPTION
SIMMS/man
SIMMS/man/dichotomize.meta.dataset.Rd SIMMS/man/get.adjacency.matrix.Rd SIMMS/man/make.matrix.Rd SIMMS/man/prepare.training.validation.datasets.Rd SIMMS/man/create.KM.plot.Rd SIMMS/man/derive.network.features.Rd SIMMS/man/create.sensitivity.plot.Rd SIMMS/man/calculate.network.coefficients.Rd SIMMS/man/load.cancer.datasets.Rd SIMMS/man/create.survobj.Rd SIMMS/man/get.program.defaults.Rd SIMMS/man/fit.coxmodel.Rd SIMMS/man/pred.survivalmodel.Rd SIMMS/man/fit.interaction.model.Rd SIMMS/man/create.classifier.multivariate.Rd SIMMS/man/SIMMS.Rd SIMMS/man/fit.survivalmodel.Rd SIMMS/man/create.classifier.univariate.Rd SIMMS/man/dichotomize.dataset.Rd SIMMS/man/create.survivalplots.Rd SIMMS/man/get.chisq.stats.Rd SIMMS/man/calculate.sensitivity.stats.Rd SIMMS/man/calculate.meta.survival.Rd

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