haplo.stats - Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.

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5.64 score 2 stars 2 dependents 118 scripts 2.0k downloads

pedgene - Gene-Level Variant Association Tests for Pedigree Data

Gene-level variant association tests with disease status for pedigree data: kernel and burden association statistics.

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3.00 score 6 scripts 459 downloads

regmed - Regularized Mediation Analysis

Mediation analysis for multiple mediators by penalized structural equation models with different types of penalties depending on whether there are multiple mediators and only one exposure and one outcome variable (using sparse group lasso) or multiple exposures, multiple mediators, and multiple outcome variables (using lasso, L1, penalties).

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openblascpp

3.00 score 2 stars 8 scripts 271 downloads

smartDesign - Sequential Multiple Assignment Randomized Trial Design

SMART trial design, as described by He, J., McClish, D., Sabo, R. (2021) <doi:10.1080/19466315.2021.1883472>, includes multiple stages of randomization, where participants are randomized to an initial treatment in the first stage and then subsequently re-randomized between treatments in the following stage.

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3.00 score 1 scripts 165 downloads

pleio - Pleiotropy Test for Multiple Traits on a Genetic Marker

Perform tests for pleiotropy of multiple traits of various variable types on genotypes for a genetic marker.

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3.00 score 9 scripts 169 downloads

vcpen - Penalized Variance Components Analysis

Method to perform penalized variance component analysis.

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openblascpp

2.70 score 1 scripts 153 downloads

fam.recrisk - Familial Recurrence Risk

Given vectors of family sizes and number of affecteds per family, calculates the risk of disease recurrence in an unaffected person, conditional on a family having at least k affected members. Methods also model heterogeneity of disease risk across families by fitting a mixture model, allowing for high and low risk families.

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1.00 score 4 scripts 167 downloads