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4 packages on CRAN

1 packages on Bioconductor

knitr

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Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

GenomicInteractions

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R package for handling Genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots / statistics.

simml

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A major challenge in estimating treatment decision rules from a randomized clinical trial dataset with covariates measured at baseline lies in detecting relatively small treatment effect modification-related variability (i.e., the treatment-by-covariates interaction effects on treatment outcomes) against a relatively large non-treatment-related variability (i.e., the main effects of covariates on treatment outcomes). The class of Single-Index Models with Multiple-Links is a novel single-index model specifically designed to estimate a single-index (a linear combination) of the covariates associated with the treatment effect modification-related variability, while allowing a nonlinear association with the treatment outcomes via flexible link functions. The models provide a flexible regression approach to developing treatment decision rules based on patients' data measured at baseline. We refer to Petkova, Tarpey, Su, and Ogden (2017) <doi: 10.1093/biostatistics/kxw035> and "A constrained single-index model for estimating interactions between a treatment and covariates" (under review, 2019) for detail. The main function of this package is simml().

simsl

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An implementation of a single-index regression for optimizing individualized dose rules from an observational study. To model interaction effects between baseline covariates and a treatment variable defined on a continuum, we employ two-dimensional penalized spline regression on an index-treatment domain, where the index is defined as a linear combination of the covariates (a single-index). An unspecified main effect for the covariates is allowed. A unique contribution of this work is in the parsimonious single-index parametrization specifically defined for the interaction effect term. We refer to Park, Petkova, Tarpey, and Ogden (2020) <doi:10.1016/j.jspi.2019.05.008> (for the case of a discrete treatment) and Park, Petkova, Tarpey, and Ogden (2019) "A single-index model with a surface-link for optimizing individualized dose rules" (pre-print) for detail of the method. The main function of this package is simsl().

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Regression-based ranking of pathogen strains with respect to their contributions to natural epidemics, using demographic and genetic data sampled in the curse of the epidemics. This package also includes the GMCPIC test.