Software Packages

Department of Quantitative Health Sciences
Mayo Clinic Research
Formerly known as the Department of Health Sciences Research

Related links: Division Overview R Shiny Applications
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armitage trend test for trait and SNP dosage Authors: Jason Sinnwell (primary contact) Dan Schaid Link: armitage_0.2.1.tar.gz Language/Platform: R


Generalized Estimating Equations for Affected Relative Pairs Authors: Dan Schaid Jason Sinnwell Link: arp.gee_0.1.1.tar.gz Language/Platform: R


An Arsenal of ‘R’ Functions for Large-Scale Statistical Summaries An Arsenal of ‘R’ functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in ‘R’ and ‘RStudio’ and which use formulas and versatile summary statistics for summary tables and models. The primary functions include tableby(), a Table-1-like summary of multiple […]


Population Attributable Risk Estimates population (etiological) attributable risk for unmatched, pair-matched or set-matched case-control designs and returns a list containing the estimated attributable risk, estimates of coefficients, and their standard errors, from the (conditional, If necessary) logistic regression used for estimating the relative risk. Authors: Beth Atkinson (primary contact) Louis Schenck Cindy Crowson Terry Therneau […]


Routines for Block Diagonal Symmetric matrices This is a special case of sparse matrices, used by coxme Authors: Terry Therneau Available at: Language/Platform: R

bilinear regression to 16O/18O isotope label experiments Authors: Doug Mahoney (primary contact) Jeanette Eckel-Passow Available at: Language/Platform: R


Mixed Effects Cox Models Cox proportional hazards models containing Gaussian random effects, also known as frailty models. Authors: Terry Therneau Available at: Language/Platform: R


Deming, Thiel-Sen and Passing-Bablock Regression Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions. Authors: Terry Therneau Available at: Language/Platform: R


Fast Loess Authors: Doug Mahoney Jeanette Eckel-Passow Ann Oberb Link: fastlo_1.3.tar.gz Language/Platform: R


Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous This software offers a suite of R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (because of unknown linkage phase of the genetic markers). The genetic markers are […]


Hardy-Weinberg Equilibrium Tests Test the fit of genotype frequencies to Hardy-Weinberg Equilibrium proportions for autosomes and the X chromosome. Different statistical tests are provided, as well as an option to evaluate statistical significance by either exact methods or simulations Authors: Jason Sinnwell (primary contact) Dan Schaid Dan Folie Link: hwe_0.3.1.tar.gz   Language/Platform: R


Regression Methods for IBD Linkage With Covariates A method to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. Authors: Jason Sinnwell (primary contact) Dan Schaid Available at: Language/Platform: R


Pedigree Functions {Pedigree Functions description} Authors: Jason Sinnwell (primary contact) Terry Therneau Beth Atkinson Dan Schaid Available at: Language/Platform: R


LD calculations on multi-allele, and SNP variants, including the composite-LD measure.


Check Pedigrees for Mendelian Errors Check Pedigrees for Mendelian Errors and, when errors are found, systematically jackknifes every typed pedigree member to determine if eliminating this member will remove all Mendelian Errors from the pedigree Authors: Jason Sinnwell (primary contact) Dan Schaid Dan Folie Link: mend.err_1.3.tar.gz Language/Platform: R


Quantitative Linkage Analysis Tools using the Variance Components Approach Calculate the polygenic and major gene models for quantitative trait linkage analysis using the variance components approach. Authors: Pat Votruba (primary contact) Beth Atkinson Mariza de Andrade Available at: Language/Platform: R


PANOPLY, a novel computational approach to integrate both germline and somatic data obtained from multi-omics platforms for an individual of interest and analyze that data in the context matched-control samples.


Gene-Level Statistics for Pedigree Data Gene-level association tests with disease status for pedigree data: kernel and burden association statistics. Authors: Jason Sinnwell (primary contact) Dan Schaid Available at: Language/Platform: R


Pleiotropy Test for Multiple Traits on a Genetic Marker Perform tests for pleiotropy of multiple traits of various variable types on genotypes for a genetic marker. Authors: Jason Sinnwell (primary contact) Dan Schaid Available at: Language/Platform: R


Sample size for RNAseq studies {Short description of project/tool (1-3 sentences)} Authors: Terry Therneau (primary contact) Steven Hart JP Kocher Available at: Publication: Language/Platform: R  


Recursive Partitioning and Regression Trees Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone. Authors: Beth Atkinson Terry Therneau Brian Ripley (primary contact) Available at: Language/Platform: R


Sequential Multiple Assignment Randomized Trial (SMART) design includes multiple stages of randomization, where participants are randomized to an initial treatment in the first stage and then subsequently re-randomized between treatments in the following stage. Includes methods for mean and variance as a function of specificity/sensitivity, and power calculations.


SpatialNorm6 Spatial normalization of Affymetrix SNP 6.0 cel file, which adjusts for spatial bias based on wavelet decomposition Authors: Chai High Seng (primary contact) Link: SpatialNorm6_1.1.tar.gz  


Stress.dfArray Calculates normalization Stress and dfArray quality for a set of arrays. Authors: Doug Mahoney (primary contact) Jeanette Eckel-Passow Available at: Stress.dfArray_1.1.tar.gz Language/Platform: R


Super Learner Prediction Implements the super learner prediction method and contains a library of prediction algorithms to be used in the super learner. Authors: Eric Polley (primary contact) LeDell van der Laan Kennedy Lendle Available at: Language/Platform: R


Survival Analysis Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models. Authors: Terry Therneau (primary contact) Available at: Language/Platform: R  


trex Package that calculates a truncated exact test for two-stage case-control studies for rare genetic variants. The first stage is for screening rare variants in only cases. If the number of case-carriers of any rare variants exceeds a user-specified threshold, then additional cases and controls are genotyped for the detected variants and carrier status of […]