Analysis Tools

ARTP2 is an R package of biological pathway analysis or pathway meta-analysis for genome-wide association studies (GWAS). It also provides tools for gene-level test as a special case. ARTP2 is an enhanced version of two previously released packages ARTP and AdaJoint.

A panel of easy-to-interpret estimable APC functions and corresponding Wald tests in R code that can be accessed through a user-friendly web tool.

A subset-based approach improves power and interpretation for combined analysis of genetic assocation studies of heterogeneous traits.

Automated Germline Variant Pathogenicity (AutoGVP) integrates ClinVar variant classification with modified InterVar classification, based on American College of Medical Genetics-Association for Molecular Pathology (ACMG-AMP) guidelines, to output germline variant classification. Using automated germline classification will reduce hands-on time and allow reproducibility of variant classification.

Bayesian model for Detecting Gene Environment interaction

BSR (Bayesian Subset Regression) is an R package that implements the Bayesian subset modeling procedure for high-dimensional generalized linear models.

The Biomarker Tools set estimates risk stratification from early biomarker data and provides strategies to advance biomarkers or other risk measures identified through case-control studies to clinical or public health applications.

CaseCohortCoxSurvival is an R package for estimating Cox model log-relative hazard and covariate-specific pure risk parameters and their variances from case-cohort data.

An R package for testing Calibration of Binary Risk Model (CBRM) using different goodness-of-fit statistics

CGEN (Case-control.Genetics) is an R package for analyzing genetic data on case-control samples, with particular emphasis on novel methods for detecting Gene-Gene and Gene-Environment interactions.

CNVfam is a software package for jointly detecting copy number variations (CNV) in nuclear families genotyped using the Illumina platform.

CompareTests is an R package to estimate agreement and diagnostic accuracy statistics for two diagnostic tests when one is conducted on only a subsample of specimens. A standard test is observed on all specimens.

Software package designed to perform a range of association tests between sets of SNPs and a phenotype.

This is a R package for rapid evaluation of extremely small p-value for resampling-based test (EXPERT).

Drs. Tongwu Zhang and Jiyeon Choi developed ezQTL, a web-based bioinformatic application to interactively visualize and analyze genetic association data such as GWAS and molecular QTLs under different linkage disequilibrium (LD) patterns. ezQTL facilitates mapping disease susceptibility regions and assists researchers in characterizing and prioritizing functional genes and variants based on the genotype-phenotype associations.

The iCARE R Package allows researchers to quickly build models for absolute risk, and apply them to estimate an individual's risk of developing disease during a specified time interval, based on a set of user defined input parameters.

IRRAD is an Excel spreadsheet that extends the “Axelson adjustment” for binary variables to adjust observed RRs for a confounding variable when exposure and confounder have multiple categories or to define those characteristics that a confounder must have to explain an observed association.

IN.power is an R package for estimating the number of susceptibility SNPs and power of future studies.

Background explanation of the Interactive Radioepidemiological Computer Program

Different approaches for handling varied error structures in studies of irradiated populations

LDlink is a suite of web-based applications to easily and efficiently interrogate linkage disequilibrium in population groups, with query flexibility and interactive visualization of results.

metapack is an R package that provides a unified formula interface for both meta-analysis and network meta-analysis. The user interface—and therefore the package—allows flexible variance-covariance modeling for multivariate meta-analysis models and univariate network meta-analysis models.

MultiAssoc is a MATLAB software package for test of association of a disease with a group of SNPs after accounting for their interaction with another group of SNPs or environmental exposures.

The purpose of the R package is to increase the efficiency and remove bias from studies to estimate the efficacy of a vaccine to prevent infection. The approach is to use information from non-vaccine-targeted strains to improve inference on vaccine effects on targeted strains.

NestedCohort is an R software package for fitting Kaplan-Meier and Cox Models to estimate standardized survival and attributable risks for studies where covariates of interest are observed on only a sample of the cohort.

PCAmatchR is an open-source R software package that enables users to match cases and controls for more accurate GWAS analyses. It converts user-provided principal components (PC) into a Mahalanobis distance metric for selecting a set of well-matched controls for each case.

PGA is a software package containing algorithms and graphical user interfaces developed in Matlab for power and sample size calculation under various genetic models and statistical constraints.

POWER V3.0 Software is used for computing sample size and power for binary outcome studies.

The R package and webtool fits Prevalence Incidence Mixture models to left-censored and irregularly interval-censored time to event data that is commonly found in screening cohorts assembled from electronic health records. Absolute and relative risk can be estimated for simple random sampling, and stratified sampling (the two approaches of superpopulation and a finite population are supported for target populations). Non-parametric (absolute risks only), semi-parametric, weakly-parametric (using B-splines), and some fully parametric (such as the logistic-Weibull) models are supported.

A subregion-based burden test for simultaneous identification of susceptibility loci and subregions in rare-variant association studies.

This R package can be used to calculate the required samples size for unconditional multivariate analyses of unmatched case-control studies. The sample sizes are for a scalar exposure effect, such as binary, ordinal or continuous exposures. The sample sizes can also be computed for scalar interaction effects. The analyses account for the effects of potential confounder variables that are also included in the multivariate logistic model.

SegCNV is a software package, implemented in C++, to detect germline copy number variations in SNP array data.

Semiparametric Kernel Independence Test (SKIT) is an R package that conducts the test of independence between two vectors when there are excess zeros.

Spatial Power is a suite of web-based applications designed to perform power calculations of spatial statistics easily and efficiently, to support accurate study design for cancer epidemiology studies.

The SubHMM model for identifying tumor subclones R Package - A hidden Markov modeling approach for identifying tumor subclones in next-generation sequencing studies.

SUITOR is an R package, an unsupervised cross-validation tool to select the optimal number of signatures for mutational signature analysis.

The PLCO Atlas is an interactive tool to facilitate data sharing with the public, which enables researchers to search for, visualize, and download aggregated association results from the PLCO genome-wide association analyses (GWAS).

TREAT is an R package for detecting complex joint effects in case-control studies. The test statistic is derived from a tree-structure model by recursive partitioning the data. Ultra-fast algorithm is designed to evaluate the significance of association between candidate gene and disease outcome

WeightCalibSurvival R Package uses weight calibration to improve efficiency for estimating pure risks from additive and Cox hazards models with two-phase designs such as nested case-control design.