Research : Software

Software information

BAMarray

Java software for microarray data. Implements Bayesian Analysis of Variance for Microarrays (BAM)

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Joint Mean-Variance Stabilization and Regularization for High Throughput Data

New R package!

An R package that stabilizes variances and also regularizes inferences using information in both the mean and the variance. Applications include high throughput “omic” data as well as other high throughput datasets.

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LDLasso

An R package that performs a linkage-disequilibrium based fusion of SNP estimates in GWAS studies with the goal of producing flatter, longer signal sites to allow weaker, correlated signal while still inducing sparsity via lasso shrinkage.

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Local Sparse Bump Hunting

Coming soon!

An R package that searches for local structures in the form of modes in high dimensional space. Sparsity is imposed via sparse principal components analysis and localness imposed by tree-based partitioning of the predictor space. Modes are then identified via a version of the patient rule induction method (PRIM). New methods for optimal PRIM hyperparameter tuning are also implemented.

randomForestSRC

Random forest for survival, regression, and classification. A unified treatment of Breiman’s random forests. Coming soon as an R-package!

randomSurvivalForest

Random survival forests for right-censored and competing risks survival data. R-software release 3.63.

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spikeslab

Spike and slab R package for high dimensional linear regression models (release 1.1.2). Uses a generalized elastic net (gnet) for variableselection. Parallel processing enabled.

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