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https://cran.r-project.org/web/packages/hapassoc/index.html
Software application using a likelihood approach to inference of haplotype and nongenetic effects and their interactions in generalized linear models of disease penetrance, when haplotype phase is unknown for some subjects. Parameter estimates are obtained by use of an expectation-maximization (EM) algorithm and standard errors are calculated using Louis'' formula. (entry from Genetic Analysis Software)
Proper citation: R/HAPASSOC (RRID:SCR_009365) Copy
http://www.chg.duke.edu/research/simla30.html
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Simulation program that generates data sets of families for use in linkage and association studies. SIMLA_3.2 is a major upgrade to versions 2.3 and 3.0 that provides the ability to simulate two disease loci and two environmental covariates. Gene-gene and gene-environment interactions may also be simulated which jointly determine the disease risk of all pedigree members.
Proper citation: SIMULA (RRID:SCR_009390) Copy
http://www.niehs.nih.gov/research/resources/software/epidemiology/tagster/
Software tool to select, evaluate and visualize LD tag SNPs for single or multiple populations. The input files can be a set of dumped genotype files from International HapMap Project (http://www.hapmap.org/) (Hapmap format) or Seattle SNPs (http://pga.gs.washington.edu/) (Prettybase format). The ouput is a set of LD tag SNPs for single or multiple populations. (entry from Genetic Analysis Software)
Proper citation: TAGSTER (RRID:SCR_009413) Copy
https://github.com/stanstrup/mwtabR
An R package that downloads and parses mwtab data from Metabolomics Workbench studies. Downloaded files are converted into R lists.
Proper citation: mwtabR (RRID:SCR_014677) Copy
http://CRAN.R-project.org/package=nlme
Software to fit and compare Gaussian linear and nonlinear mixed-effects models.
Proper citation: R package: nlme (RRID:SCR_015655) Copy
https://github.com/Eroglu-Lab/In-Vitro-Sholl.git
Software R analysis code for analyzing fluorescence microscopy images to determine complexity of cultured astrocytes. Sholl profile analysis based on mixed-effect models.
Proper citation: In-Vitro-Sholl (RRID:SCR_025662) Copy
http://www.bioconductor.org/packages/release/bioc/html/ncdfFlow.html
Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data.
Proper citation: ncdfFlow (RRID:SCR_000009) Copy
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