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Discovering the causes of cancer and the means of prevention

Tools & Resources

Biostatistics Branch investigators develop statistical and computational tools for epidemiologic and laboratory studies, and distribute those tools to collaborators and the greater scientific community.

BB Descriptive Epidemiology Resources
  • Age Period Cohort 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.

BB Risk Assessment Tools
BB Analysis Tools
  • Age Period Cohort 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.

  • Adaptive Rank Truncated Product - Version 2 (ARTP2)

    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.

  • Association analysis based on SubSETs (ASSET)

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

  • 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 high-dimensional generalized linear models.

  • CBRM

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

  • CGEN R Package

    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

    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 Resampling-based Test

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

  • Het-Tree

    This is the R package implementing the testing procedure described in the referred manuscript

  • 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 specifed time interval, based on a set of user defined input parameters.

  • INPower

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

  • KinCohort

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

  • 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.

  • Nested Cohort

    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.

  • segCNV

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

  • TREAT (TREe-based Association Test)

    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

BB Study Design & Planning Tools
  • POWER V3.0 Software

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

  • 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.