Showing 6 of total 6 results (show query)
bioc
snpStats:SnpMatrix and XSnpMatrix classes and methods
Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.
Maintained by David Clayton. Last updated 5 months ago.
microarraysnpgeneticvariabilityzlib
74.0 match 9.41 score 674 scripts 17 dependents
cran
TriadSim:Simulating Triad Genomewide Genotypes
Simulate genotypes for case-parent triads, case-control, and quantitative trait samples with realistic linkage diequilibrium structure and allele frequency distribution. For studies of epistasis one can simulate models that involve specific SNPs at specific sets of loci, which we will refer to as "pathways". TriadSim generates genotype data by resampling triad genotypes from existing data. The details of the method is described in the manuscript under preparation "Simulating Autosomal Genotypes with Realistic Linkage Disequilibrium and a Spiked in Genetic Effect" Shi, M., Umbach, D.M., Wise A.S., Weinberg, C.R.
Maintained by Min Shi. Last updated 4 years ago.
10.0 match 3.00 scorebioc
GWASTools:Tools for Genome Wide Association Studies
Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.
Maintained by Stephanie M. Gogarten. Last updated 5 months ago.
snpgeneticvariabilityqualitycontrolmicroarray
2.3 match 17 stars 10.50 score 396 scripts 5 dependents
jiscah
sequoia:Pedigree Inference from SNPs
Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.
Maintained by Jisca Huisman. Last updated 9 months ago.
pedigreepedigree-reconstructionpedigreessequoiasnpsnp-datafortran
3.0 match 26 stars 7.40 score 79 scripts
ochoalab
genio:Genetics Input/Output Functions
Implements readers and writers for file formats associated with genetics data. Reading and writing Plink BED/BIM/FAM and GCTA binary GRM formats is fully supported, including a lightning-fast BED reader and writer implementations. Other functions are 'readr' wrappers that are more constrained, user-friendly, and efficient for these particular applications; handles Plink and Eigenstrat tables (FAM, BIM, IND, and SNP files). There are also make functions for FAM and BIM tables with default values to go with simulated genotype data.
Maintained by Alejandro Ochoa. Last updated 24 days ago.
2.0 match 17 stars 7.97 score 213 scripts 4 dependentsbioc
gwascat:representing and modeling data in the EMBL-EBI GWAS catalog
Represent and model data in the EMBL-EBI GWAS catalog.
Maintained by VJ Carey. Last updated 5 months ago.
1.6 match 6.05 score 110 scripts 2 dependents