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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Benjamin Haibe-Kains

Publications for survcomp

survcomp citations

 (18)
library_books

Molecular and clinical features of the TP53 signature gene expression profile in early stage breast cancer

2018
Oncotarget
PMCID: 5865663
PMID: 29581837
DOI: 10.18632/oncotarget.24447

[…] used 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 []. […]

library_books

Decoding critical long non coding RNA in ovarian cancer epithelial to mesenchymal transition

2017
Nat Commun
PMCID: 5693921
PMID: 29150601
DOI: 10.1038/s41467-017-01781-0

[…] genes. Differential gene expression P-values, obtained from the multiple independent data sets, were summarized by computing the Fisher’s combined probability test by using the R/Bioconductor package Survcomp. The P-values represent overall significance of the differential expression of these important genes inferred from multiple independent data sets. Collectively, the results indicate that DNM3 […]

call_split

Limits of radiomic based entropy as a surrogate of tumor heterogeneity: ROI area, acquisition protocol and tissue site exert substantial influence

2017
Sci Rep
PMCID: 5554130
PMID: 28801575
DOI: 10.1038/s41598-017-08310-5
call_split See protocol

[…] Meier method. We computed the concordance index for validating the predictive ability of a model based on the increase in entropy for the prediction of overall survival. For this we used the package survcomp from Bioconductor. Statistical analyses were performed using R version 3.3.0 and SPSS 24.0. […]

library_books

Validation of Nomograms for Survival and Metastases after Hysterectomy and Adjuvant Therapy in Uterine Cervical Cancer with Risk Factors

2017
Biomed Res Int
PMCID: 5425848
PMID: 28536694
DOI: 10.1155/2017/2917925

[…] SPSS Inc., Chicago, IL) was used to evaluate the log-rank tests and the Cox-regression multivariate analyses. The R software version 3.3.2 was used for the calculation of the C-index. Using packages “survcomp” and “compareC” of the R software version 3.3.2, each C-index was calculated and the C-indies of nomograms scores and our Cox-regression models for each survival were compared, respectively. […]

library_books

A Practical Guide to Visualization and Statistical Analysis of R. solanacearum Infection Data Using R

2017
Front Plant Sci
PMCID: 5401893
PMID: 28484483
DOI: 10.3389/fpls.2017.00623

[…] (), dplyr (), ggplot2 (), modelr () and stringr () [these and other helpful packages are part of the tidyverse ()].Functions from the following packages are used for analysis: MESS (), survival (; ), survcomp (; ), rms (, ), coxme (), lme4 (), lmerTest (), multcomp (), and rcompanion ().To able to work with the Supplementary “R Markdown” (.Rmd) files, the packages rmarkdown () and knitr (, , ) are […]

library_books

Squalene epoxidase is a bona fide oncogene by amplification with clinical relevance in breast cancer

2016
Sci Rep
PMCID: 4726025
PMID: 26777065
DOI: 10.1038/srep19435

[…] els respectively, using the Tukey honest significant difference method to compare levels in the latter case. Survival curves were plotted using the Kaplan-Meier estimators, generated with the package survcomp, and P values were calculated with the log-rank test. For survival analyses including more than one variable, a stepwise backward-forward Cox proportional hazards regression model was employe […]


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

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