Analysis Tools

ARTP

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

APC Analysis Web tool

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.

ASSET

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

Automated Germline Variant Pathogenicity (AutoGVP)

AutoGVP integrates ClinVar variant classification with modified InterVar classification to output germline variant classification.

BaDGE

Bayesian model for Detecting Gene Environment interaction

BSR

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

Biomarker Tools

Web-based tools to estimate risk stratification and provide strategies to advance biomarkers or other risk measures to clinical or public health applications.

CaseCohortCoxSurvival R-Package

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.

CBRM

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

CGEN

CGEN (Case-control.Genetics) is an R package for analyzing genetic data on case-control samples.

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.

CRaVe

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

EXPERT

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

Interactive Visualization and Colocalization of Quantitative Trait Loci

Interactively visualize and analyze genetic association data and molecular QTLs under different linkage disequilibrium patterns.

iCARE

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 specifed 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 (measured or unmeasured) confounding variable when exposure and confounder have multiple categories.

INPower

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

Interactive Radioepidemiological Computer Program

Background explanation of the Interactive Radioepidemiological Computer Program

KinCohort

KinCohort is a MATLAB software package for likelihood-based analysis of kin-cohort data

LDlink

Web-based applications to easily and efficiently interrogate linkage disequilibrium in populations

metapack R Package

R package that provides a unified formula interface for both meta-analysis and network meta-analysis.

Negative Control Outcome Adjustment - R Package

R-package: Methods to reduce confounding bias from unmeasured confounders in observational studies of vaccine efficacy using negative control outcomes.

Nested Cohort

NestedCohort: R package for Kaplan-Meier and Cox Models to estimate standardized survival, attributable risks for covariates observed in a sample of the cohort

PCAmatchR: Match Cases to Controls

PCAmatchR enables users to match cases and controls for more accurate GWAS analyses.

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

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

Prevalence Incidence Mixture Models

R package and webtool fits Prevalence Incidence Mixture models for data in screening cohorts assembled from electronic health records

REBET

A Subregion-based Burden Test for Simultaneous Identification of Susceptibility Loci and Sub-regions in Rare-variant Association Studies.

Sample size calculations for case-control studies

This R package can be used to calculate the required samples size for unconditional multivariate analyses of unmatched case-control studies.

Semiparametric Kernel Independence Test (SKIT)

SKIT is an R package that conducts the test of independence between two vectors when there are excess zeros.

Spatial Power

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

subHMM - Model for Identifying Tumor Subclones R Package

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

SUITOR

Selecting the Number of Mutational Signatures through Cross-Validation

PLCO Atlas, GWAS Explorer

Interactive access to GWAS data from 110,562 PLCO participants.

TREAT (TREe-based Association Test)

TREAT (TREe-based Association Test) version 0.0.5 is an R package for detecting complex joint effects in case-control studies

WeightCalibSurvival R Package

To improve efficiency for estimating pure risks from additive hazards and Cox proportional hazards models with nested case-control designs