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gap - Genetic Analysis Package

As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

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geneticsimputationlmm

12.39 score 13 stars 24 dependents 522 scripts 27k downloads

gap.datasets - Datasets for 'gap'

Datasets associated with the 'gap' package. Currently, it includes an example data for regional association plot (CDKN), an example data for a genomewide association meta-analysis (OPG), data in studies of Parkinson's diease (PD), ALHD2 markers and alcoholism (aldh2), APOE/APOC1 markers and Schizophrenia (apoeapoc), cystic fibrosis (cf), a Olink/INF panel (inf1), Manhattan plots with (hr1420, mhtdata) and without (w4) gene annotations.

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geneticsimputationlmm

9.26 score 13 stars 25 dependents 8 scripts 20k downloads

pan - Multiple Imputation for Multivariate Panel or Clustered Data

It provides functions and examples for maximum likelihood estimation for generalized linear mixed models and Gibbs sampler for multivariate linear mixed models with incomplete data, as described in Schafer JL (1997) "Imputation of missing covariates under a multivariate linear mixed model". Technical report 97-04, Dept. of Statistics, The Pennsylvania State University.

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8.11 score 1 stars 188 dependents 83 scripts 56k downloads

lmm - Linear Mixed Models

Implements Expectation/Conditional Maximization Either (ECME), rapidly converging algorithms, and Bayesian inference for linear mixed models following Schafer (1998), "Some Improved Procedures for Linear Mixed Models", Department of Statistics, The Pennsylvania State University.

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geneticsimputationlmm

7.02 score 13 stars 12 scripts 315 downloads

tdthap - TDT Tests for Extended Haplotypes

Functions and examples for transmission/disequilibrium tests for extended marker haplotypes, as described in Clayton and Jones (1999) <doi:10.1086/302566>.

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geneticsimputationlmm

6.09 score 13 stars 7 scripts 378 downloads

gaawr2 - Genetic Association Analysis

This is a companion to Henry-Stewart talk by Zhao (2026, <doi:10.69645/FRFQ9519>), which gathers information, metadata and scripts to showcase modern genetic analysis -- ranging from testing of polymorphic variant(s) for Hardy-Weinberg equilibrium, association with traits using genetic and statistical models, Bayesian implementation, power calculation in study design, and genetic annotation. It also covers R integration with the Linux environment, GitHub, package creation and web applications. The earlier version by Zhao (2009, <doi:10.69645/DCRY5578>) provides a brief introduction to these topics.

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4.78 score 5 scripts 514 downloads

pQTLdata - A Collection of Proteome Panels and Metadata

It aggregates protein panel data and metadata for protein quantitative trait locus (pQTL) analysis using 'pQTLtools' (<https://jinghuazhao.github.io/pQTLtools/>). The package includes data from affinity-based panels such as 'Olink' (<https://olink.com/>) and 'SomaScan' (<https://somalogic.com/>), as well as mass spectrometry-based panels from 'CellCarta' (<https://cellcarta.com/>), 'Seer' (<https://seer.bio/>) and 'SWATH-MS' (<doi:10.15252/msb.20178126>). The metadata encompasses updated annotations and publication details.

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3.48 score 3 stars 4 scripts 290 downloads