Analysis Tools
Analysis Tools
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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
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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.
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ASSET
A subset-based approach improves power and interpretation for combined analysis of genetic assocation studies of heterogeneous traits.
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Automated Germline Variant Pathogenicity (AutoGVP)
AutoGVP integrates ClinVar variant classification with modified InterVar classification to output germline variant classification.
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BaDGE
Bayesian model for Detecting Gene Environment interaction
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BSR
BSR (Bayesian Subset Regression) is an R package that implements the Bayesian subset modeling procedure for high-dimensional generalized linear models.
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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.
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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.
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CBRM
An R package for testing Calibration of Binary Risk Model (CBRM) using different goodness-of-fit statistics
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CGEN
CGEN (Case-control.Genetics) is an R package for analyzing genetic data on case-control samples.
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CNVfam
CNVfam is a software package for jointly detecting copy number variations (CNV) in nuclear families genotyped using the Illumina platform.
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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.
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CRaVe
Software package designed to perform a range of association tests between sets of SNPs and a phenotype.
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EXPERT
This is a R package for rapid evaluation of extremely small p-value for resampling-based test (EXPERT).
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Interactive Visualization and Colocalization of Quantitative Trait Loci
Interactively visualize and analyze genetic association data and molecular QTLs under different linkage disequilibrium patterns.
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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.
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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.
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INPower
IN.power is an R package for estimating the number of susceptibility SNPs and power of future studies.
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Interactive Radioepidemiological Computer Program
Background explanation of the Interactive Radioepidemiological Computer Program
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KinCohort
KinCohort is a MATLAB software package for likelihood-based analysis of kin-cohort data
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LDlink
Web-based applications to easily and efficiently interrogate linkage disequilibrium in populations
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metapack R Package
R package that provides a unified formula interface for both meta-analysis and network meta-analysis.
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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.
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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
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PCAmatchR: Match Cases to Controls
PCAmatchR enables users to match cases and controls for more accurate GWAS analyses.
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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.
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POWER V3.0
POWER V3.0 Software is used for computing sample size and power for binary outcome studies.
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Prevalence Incidence Mixture Models
R package and webtool fits Prevalence Incidence Mixture models for data in screening cohorts assembled from electronic health records
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REBET
A Subregion-based Burden Test for Simultaneous Identification of Susceptibility Loci and Sub-regions in Rare-variant Association Studies.
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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.
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Semiparametric Kernel Independence Test (SKIT)
SKIT is an R package that conducts the test of independence between two vectors when there are excess zeros.
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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.
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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.
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SUITOR
Selecting the Number of Mutational Signatures through Cross-Validation
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PLCO Atlas, GWAS Explorer
Interactive access to GWAS data from 110,562 PLCO participants.
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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
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WeightCalibSurvival R Package
To improve efficiency for estimating pure risks from additive hazards and Cox proportional hazards models with nested case-control designs