Analysis Tools

Adaptive Rank Truncated Product  Version 2 (ARTP2)
ARTP2 is an R package of biological pathway analysis or pathway metaanalysis for genomewide association studies (GWAS). It also provides tools for genelevel test as a special case. ARTP2 is an enhanced version of two previously released packages ARTP and AdaJoint.

Age Period Cohort Analysis Web Tool
A panel of easytointerpret estimable APC functions and corresponding Wald tests in R code that can be accessed through a userfriendly web tool.

Association analysis based on SubSETs (ASSET)
A subsetbased approach improves power and interpretation for combined analysis of genetic assocation studies of heterogeneous traits.

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

BaDGE (Bayesian model for Detecting Gene Environment interaction)
Bayesian model for Detecting Gene Environment interaction

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

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

CaseCohortCoxSurvival: CaseCohort Cox Survival Inference RPackage
CaseCohortCoxSurvival is an R package for estimating Cox model logrelative hazard and covariatespecific pure risk parameters and their variances from casecohort data.

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

CGEN R Package
CGEN (Casecontrol.Genetics) is an R package for analyzing genetic data on casecontrol samples, with particular emphasis on novel methods for detecting GeneGene and GeneEnvironment interactions.

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

CompareTests
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.

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

Extremely small Pvalue Evaluation for Resamplingbased Test
This is a R package for rapid evaluation of extremely small pvalue for resamplingbased test (EXPERT).

ezQTL: Web Platform for Interactive Visualization and Colocalization of Quantitative Trait Loci (QTL) and GWAS
Drs. Tongwu Zhang and Jiyeon Choi developed ezQTL, a webbased 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 genotypephenotype associations.

iCARE: An R Package to Compute Individualized Coherent Absolute Risk Estimators
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.

Indirect Relative Risk Adjustment (IRRAD)
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.

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

Interactive Radioepidemiological Computer Program (IRCP)
Background explanation of the Interactive Radioepidemiological Computer Program

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

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

metapack: An R Package for Bayesian MetaAnalysis and Network MetaAnalysis with a Unified Formula Interface
metapack is an R package that provides a unified formula interface for both metaanalysis and network metaanalysis. The user interface—and therefore the package—allows flexible variancecovariance modeling for multivariate metaanalysis models and univariate network metaanalysis models.

MultAssoc
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.

Negative Control Outcome Adjustment  R Package
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 nonvaccinetargeted strains to improve inference on vaccine effects on targeted strains.

Nested Cohort
NestedCohort is an R software package for fitting KaplanMeier 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: Match Cases to Controls Based on Genotype Principal Components
PCAmatchR is an opensource R software package that enables users to match cases and controls for more accurate GWAS analyses. It converts userprovided principal components (PC) into a Mahalanobis distance metric for selecting a set of wellmatched controls for each case.

Power for Genetic Association Analyses (PGA)
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
POWER V3.0 Software is used for computing sample size and power for binary outcome studies.

Prevalence Incidence Mixture Models
The R package and webtool fits Prevalence Incidence Mixture models to leftcensored and irregularly intervalcensored 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). Nonparametric (absolute risks only), semiparametric, weaklyparametric (using Bsplines), and some fully parametric (such as the logisticWeibull) models are supported.

REBET
A subregionbased burden test for simultaneous identification of susceptibility loci and subregions in rarevariant association studies.

Sample size calculations for casecontrol studies
This R package can be used to calculate the required samples size for unconditional multivariate analyses of unmatched casecontrol 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
SegCNV is a software package, implemented in C++, to detect germline copy number variations in SNP array data.

Semiparametric Kernel Independence Test (SKIT)
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: Estimate Statistical Power of Spatial Clusters
Spatial Power is a suite of webbased applications designed to perform power calculations of spatial statistics easily and efficiently, to support accurate study design for cancer epidemiology studies.

subHMM
The SubHMM model for identifying tumor subclones R Package  A hidden Markov modeling approach for identifying tumor subclones in nextgeneration sequencing studies.

SUITOR: Selecting the Number of Mutational Signatures through CrossValidation
SUITOR is an R package, an unsupervised crossvalidation tool to select the optimal number of signatures for mutational signature analysis.

The PLCO Atlas, GWAS Explorer
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 genomewide association analyses (GWAS).

TREAT (TREebased Association Test)
TREAT is an R package for detecting complex joint effects in casecontrol studies. The test statistic is derived from a treestructure model by recursive partitioning the data. Ultrafast algorithm is designed to evaluate the significance of association between candidate gene and disease outcome

WeightCalibSurvival R Package
WeightCalibSurvival R Package uses weight calibration to improve efficiency for estimating pure risks from additive and Cox hazards models with twophase designs such as nested casecontrol design.