Software

Natural Language Processing

• NILE
  Fast natural language processing for electronic health records
• EXTEND [ GitHub ]
  Extraction of numerical data from electronic medical records
• CHANL [ GitHub ]
  Chart review tool powered by natural language processing

Electronic Health Records

• PheCAP [ GitHub | CRAN ]
  High-throughput phenotyping using a common semi-supervised approach
• PheNorm [ GitHub | CRAN ]
  Phenotyping algorithm that does not require expert-labeled samples for training
• MAP [ GitHub | CRAN ]
  High-throughput multimodal automated phenotyping
• sureLDA [ GitHub | CRAN ]
  Multidisease automated phenotyping method for the electronic health records
• KESER [ GitHub ]
  Clinical knowledge extraction via sparse embedding regression
• SCORNET [ GitHub | CRAN ]
  Semi-supervised calibration of risk with noisy event times
• SAMGEP [ GitHub | CRAN ]
  Semi-supervised adaptive Markov Gaussian embedding process
• MASTA [ GitHub ]
  Multi-modal automated survival time annotation

High Dimensional Inference

• StructureMC [ GitHub | CRAN ]
  Structured matrix completion with applications to genomic data integration
• solid [ GitHub ]
  Divide-and-conquer method for sparse risk prediction and evaluation
• dcalasso [ GitHub ]
  Fast divide-and-conquer sparse Cox regression
• SRAT [ GitHub ]
  Sequence robust association test for familial data

Survival Analysis

• PanelCurrentStatus [ GitHub ]
  Developing and evaluating risk prediction models with panel current status data
• survAccuracyMeasures [ GitHub ]
  Accuracy measures for risk prediction markers with survival data
• survCompetingRisk [ GitHub ]
  Prognostic accuracy of a marker with multiple competing risk events
• survMarkerTwoPhase [ GitHub ]
  Prognostic accuracy of a marker under two phase designs
• survNRI [ GitHub ]
  Evaluating incremental values from new predictors with net reclassification improvement

Surrogate Marker

• OptimalSurrogate [ GitHub | CRAN ]
  Model free approach to quantifying surrogacy
• SurrogateOutcome [ CRAN ]
  Estimation of the proportion of treatment effect explained by surrogate outcome information
• SurrogateTest [ CRAN ]
  Early testing for a treatment effect using surrogate marker informationd