Difference between revisions of "Biobanking Tools"

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|-
 
| Imputation
 
| Imputation
| [http://mathgen.stats.ox.ac.uk/impute/impute.html Impute]
+
| [http://www.sph.umich.edu/csg/abecasis/MACH MACH]
| Impute is a program for estimating unobserved genotypes in SNP association studies
+
| MACH 1.0 is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.
| None
+
| ([http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18958166 pubmed])
 
|-
 
|-
 
| Imputation
 
| Imputation
| [http://faculty.washington.edu/browning/beagle/beagle.html BEAGLE]
+
| [http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/fastPHASE.php fastPHASE]
| Analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples.
+
| The program fastPHASE implements methods for estimating haplotypes and missing genotypes from population SNP genotype data.  
| None
+
| ([http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18958166 pubmed])
 
|-
 
|-
 
| Imputation
 
| Imputation
| [http://www.sph.umich.edu/csg/abecasis/MACH MACH]
+
| [http://mathgen.stats.ox.ac.uk/impute/impute.html IMPUTE]
| Markov Chain based Haplotyper to resolve long haplotypes or infer missing genotypes in samples of unrelated individuals
+
| IMPUTE is a program for imputing unobserved genotypes in genome-wide case-control studies based on a set of known haplotypes (like the HapMap Phase II haplotypes).
| None
+
| ([http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18958166 pubmed])
 +
|-
 +
| Imputation
 +
| [http://pngu.mgh.harvard.edu/purcell/plink/download.shtml PLINK]
 +
| PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
 +
| ([http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18958166 pubmed])
 +
|-
 +
| Imputation
 +
| [http://faculty.washington.edu/browning/beagle/beagle.html Beagle]
 +
| BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples.
 +
| ([http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18958166 pubmed])
 
|-
 
|-
 
| Ontology
 
| Ontology

Revision as of 15:22, 23 March 2011

Category Package Description Performance experience
GWAS GenABEL Genome Wide SNP association analysis in R None
Imputation MACH MACH 1.0 is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. (pubmed)
Imputation fastPHASE The program fastPHASE implements methods for estimating haplotypes and missing genotypes from population SNP genotype data. (pubmed)
Imputation IMPUTE IMPUTE is a program for imputing unobserved genotypes in genome-wide case-control studies based on a set of known haplotypes (like the HapMap Phase II haplotypes). (pubmed)
Imputation PLINK PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. (pubmed)
Imputation Beagle BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. (pubmed)
Ontology OntoCAT Toolkit to easily retrieve ontology terms for phenotype annotation from public Ontology resources OLS and Bioportal and from local files. Extensive.