survcomp protocols

View survcomp computational protocol

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survcomp specifications

Information


Unique identifier OMICS_02373
Name survcomp
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.30.0
Stability Stable
Requirements
stats, grid, graphics, Biobase, survival, KernSmooth, xtable, Hmisc, prodlim, R(>=3.4), ipred, SuppDists, survivalROC, bootstrap, rmeta, CPE, clinfun
Maintained Yes

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Maintainer


  • person_outline Benjamin Haibe-Kains <>

Publications for survcomp

survcomp in pipelines

 (3)
2018
PMCID: 5908308
PMID: 29682207
DOI: 10.18632/oncotarget.24907

[…] aligned with the 4 ec categories identified by the tcga [] by calculating individual mutation frequencies in each race and each identified scna group., kaplan-meier survival was performed using the survcomp package in r []. overall survival (os) was compared between each scna grouping. overall survival was defined using the ‘days_to_last_follow-up’ parameter in the tcga metadata. p values […]

2017
PMCID: 5503562
PMID: 28454104
DOI: 10.18632/oncotarget.16961

[…] were conducted with two-sided wilcox tests via the base ‘stats’[] (version 3.2.1) package wilcox.test function. pi-survival associations were determined using ‘survival’ [, ] (version 2.38-3) and ‘survcomp’ [, ] (version 1.18.0) packages. cox regressions were performed with the coxph function to regress overall patient survival on pi and wald test p-values were reported. kaplan-meier curves […]

2016
PMCID: 4977720
PMID: 27502180
DOI: 10.1186/s12885-016-2659-5

[…] for 141 patients with imaging data, and was downloaded from cbioportal on april 3, 2015. prognostic associations of volumetric features were assessed with the concordance index (ci) using the ‘survcomp’ package in bioconductor []. all statistical analyses were carried out using r version 3.1.0 [] on a linux operating system., to investigate which biological processes drive volumetric tumor […]


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survcomp in publications

 (59)
PMCID: 5908308
PMID: 29682207
DOI: 10.18632/oncotarget.24907

[…] aligned with the 4 ec categories identified by the tcga [] by calculating individual mutation frequencies in each race and each identified scna group., kaplan-meier survival was performed using the survcomp package in r []. overall survival (os) was compared between each scna grouping. overall survival was defined using the ‘days_to_last_follow-up’ parameter in the tcga metadata. p values […]

PMCID: 5832210
PMID: 29494598
DOI: 10.1371/journal.pone.0192859

[…] for which the predicted and actual outcome are concordant, ranging from a random 0.5 to a perfect 1 []., all statistical analysis was conducted in r (version 2.15.2), using the libraries: survival, survcomp, glmnet, cvtols and rms []. the development cohort is publicly available at at www.cancerdata.org and dryad (doi:10.5061/dryad.752153b)., gives a complete overview of patients […]

PMCID: 5865663
PMID: 29581837
DOI: 10.18632/oncotarget.24447

[…] to calculate risk scores []. predictive performances for rfs were compared using risk scores oftp53 signature, mammaprint, oncotypedx, and pam50. concordance index calculated using the r package survcomp was used to compare predictive performance []. intrinsic subtype by pam50 was defined using genefu version 2.6.0 with the rna-seq count data []., all tcga data was retrieved from cbioportal […]

PMCID: 5753474
PMID: 29301506
DOI: 10.1186/s12885-017-3939-4

[…] genes of the yang pathways were the yang genes. the yin yang gene expression mean ratio (ymr) signature [–] was tested using the tnbc samples of the tcga and metabric datasets by the r package survcomp., among the 4729 curated canonical pathways, and using the tcga dataset, 191 yin pathways were discovered among the seven breast cancer groups where the fdr is less than 0.1 in at least one […]

PMCID: 5806102
PMID: 29282891
DOI: 10.1002/cam4.1303

[…] the same cutoff value. we also compared the prognostic accuracy of prgps with two existing molecular signatures in terms of time‐dependent area under roc curve (auc) and concordance index (c‐index) (survcomp, version 1.22.0 and comparec, version 1.3.1) ., to identify potential biological processes related with the risk based on the prgps signature, gene set enrichment analysis (gsea) […]


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survcomp institution(s)
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA

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