Biomedical Statistics and Informatics Software Packages


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All | Alignment | Assemblers | ChIP | Copy Number Variants | Exome | Mate Pair | Methylation | Microbiome | Pathway Analysis | Proteins | RNA | SNP/SNV | Structural Variants | Visualization | R Packages | SAS Macros | Survival Analysis

comprisk

Cumulative incidence in the presence of competing risks.

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coxme

Mixed Effects Cox Models Cox proportional hazards models containing Gaussian random effects, also known as frailty models. Authors: Terry Therneau Available at: https://cran.r-project.org/web/packages/coxme/index.html Language/Platform: R

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criskcox

Competing risk survival analysis with covariates.

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findcut

Uses the method of Contal and O’Quigley (1999) to find the best cutpoint in a continuous variable with regards to a survival outcome.

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nesttest

Conducts likelihood ratio tests for nested logistic and Cox proportional hazards models.

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newsurv

Uses Graph Template Language to create a highly customizabile Kaplan-Meier curve.

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rpart

Recursive Partitioning and Regression Trees Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone. Authors: Beth Atkinson Terry Therneau Brian Ripley (primary contact) Available at: https://cran.r-project.org/web/packages/rpart/index.html Language/Platform: R

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schoen

Schoenfeld residuals for proportional hazards model.

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surv

Complete Kaplan-Meier survival analysis with printing options and logrank statistic.

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survcstd

Calculates the c-statistic (concordance, discrimination index) for survived data with time dependent covariates

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survival

Survival Analysis Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models. Authors: Terry Therneau (primary contact) Available at: https://cran.r-project.org/web/packages/survival/index.html https://github.com/therneau/survival Language/Platform: R  

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survlt

General survival statistics p(t), standard error, confidence limits, and median survival time, for the left-truncated survival analyses.

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survplot

Creates high-quality and easily customized Kaplan-Meier plots.

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