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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.cs.cmu.edu/~genome/FAST-MAP.html
Fluorescent allele-calling software toolkit: a computer software for fully automated microsatellite genotyping. (entry from Genetic Analysis Software)
Proper citation: FASTMAP (1) (RRID:SCR_008346) Copy
Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SOAP (RRID:SCR_000689) Copy
https://cran.r-project.org/web/packages/LDheatmap/index.html
Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software)
Proper citation: LDHEATMAP (RRID:SCR_006312) Copy
http://wpicr.wpic.pitt.edu/WPICCompGen/hclust/hclust.htm
Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: HCLUST (RRID:SCR_009154) Copy
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