Biomedical Statistics and Informatics Software Packages


Go to...
Software Packages
Division Overview
Suggested Searches...
All | Alignment | Assemblers | ChIP | Copy Number Variants | Exome | Mate Pair | Methylation | Microbiome | Pathway Analysis | Proteins | RNA | SNP/SNV | Structural Variants | Visualization | R Packages | SAS Macros | Survival Analysis

armitage

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

Read more...

arp.gee

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

Read more...

Arsenal

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 […]

Read more...

Attribrisk

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 […]

Read more...

bdsmatrix

Routines for Block Diagonal Symmetric matrices This is a special case of sparse matrices, used by coxme Authors: Terry Therneau Available at: https://cran.r-project.org/web/packages/bdsmatrix/index.html Language/Platform: R

Read more...

bilinear.fit

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

Read more...

coxme

Mixed Effects Cox Models Cox proportional hazards models containing Gaussian random effects, also known as frailty models. Authors: Terry Therneau Available at: https://cran.r-project.org/web/packages/coxme/index.html Language/Platform: R

Read more...

deming

Deming, Thiel-Sen and Passing-Bablock Regression Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions. Authors: Terry Therneau Available at: https://cran.r-project.org/web/packages/deming/index.html Language/Platform: R

Read more...

fastlo

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

Read more...

haplo.stats

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 […]

Read more...

hwe

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

Read more...

ibdreg

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: https://cran.r-project.org/web/packages/ibdreg/index.html Language/Platform: R

Read more...

kinship2

Pedigree Functions {Pedigree Functions description} Authors: Jason Sinnwell (primary contact) Terry Therneau Beth Atkinson Dan Schaid Available at: https://cran.r-project.org/web/packages/kinship2/index.html Language/Platform: R

Read more...

ld.pairs

LD measure on multi-allele variants LD calculations on multi-allele, and SNP variants, including the composite-LD measure. Authors: Jason Sinnwell (primary contact) Dan Schaid Available at: /data5/bsi/adhoc/s200555.R-infrastructure/localrepo/R-3.3.1/ Language/Platform:

Read more...

mend.err

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

Read more...

multic

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: https://cran.r-project.org/web/packages/multic/index.html Language/Platform: R

Read more...

Panoply

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.

Read more...

pedgene

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: https://cran.r-project.org/web/packages/pedgene/index.html Language/Platform: R

Read more...

pleio

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: https://cran.r-project.org/web/packages/pleio/index.html Language/Platform: R

Read more...

RNASeqPower

Sample size for RNAseq studies {Short description of project/tool (1-3 sentences)} Authors: Terry Therneau (primary contact) Steven Hart JP Kocher Available at: https://bioconductor.org/packages/release/bioc/html/RNASeqPower.html Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842884/ Language/Platform: R  

Read more...

rpart

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: https://cran.r-project.org/web/packages/rpart/index.html Language/Platform: R

Read more...

SpatialNorm6

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  

Read more...

Stress.dfArray

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

Read more...

SuperLearner

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: https://cran.r-project.org/web/packages/SuperLearner/index.html https://github.com/ecpolley/SuperLearner Language/Platform: R

Read more...

survival

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: https://cran.r-project.org/web/packages/survival/index.html https://github.com/therneau/survival Language/Platform: R  

Read more...

trex

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 […]

Read more...