PheCAP

High-throughput phenotyping with electronic medical record data using a common semi-supervised approach

MAP

High-throughput multimodal automated phenotyping with application to PheWAS

NILE

Narrative information linear extraction software for natural language processing

CHANL

Provides the full name or a short summary of the software here

EXTEND

Provides the full name or a short summary of the software here

OptimalSurrogate

Model free approach to quantifying the proportion of treatment effect explained by a surrogate marker

SurrogateOutcome

Estimation of the proportion of treatment effect explained by surrogate outcome information

SurrogateTest

Early testing for a treatment effect using surrogate marker information

survAccuracyMeasures

Estimate accuracy measures for risk prediction markers with survival data

survMarkerTwoPhase

Evaluate the prognostic accuracy of a marker under two phase designs

survCompetingRisk

Evaluate the prognostic accuracy of a marker with multiple competing risk events

survNRI

Calculate the net reclassification improvement for survival data

PanelCurrentStatus

Risk Prediction Models with Panel Current Status Data

Power Calculation Apps

Shiny web applications to simulate power for prognostic biomarker validation studies with time to event data

• Cohort data
• Case-cohort design
• Nested case-control design

StructureMC

Structured matrix completion with applications to genomic data integration

dcalasso

Fast divide-and-conquer Cox proportional hazards model with adaptive lasso