- QTL mapping pipeline
- Genotype Harmonizer
- Genotype IO
- GADO Command line
- GeneNetwork Analysis
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This Systems Genetics repository contains several of the tools developed by the University Medical Center Groningen at the Genetics Department and the Genomics Coordination Center.
A high speed QTL mapping tool allowing large scale meta-analysis. We also have an Allele Specific Expression analysis module.
- Analysis plan eQTL meta analysis: eQTL mapping analysis cookbook
- Analysis plan eQTL meta analysis: meQTL mapping analysis cookbook
The Genotype Harmonizer (GH) is an easy to use command line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.
Linkage disequilibrium (LD) patterns are used to determine the correct strand GC and AT SNPs and by using the Genotype IO API we can import and export different file formats.
More info can be found here
The GH can be downloaded here
The Genotype IO API is a JAVA library that allows accessing genotype data form difference sources in a uniform and fast manner. More information can be found here
The ASE package is a command line tool to asses allele specific expression in RNA seq data. More information on ASE can be found here and a precompiled tool can be downloaded here.
Decon2 is a statistical framework for estimating cell counts using molecular profiling such as expression or methylation data from heterogeneous samples (Decon-cell) and consecutive
deconvolution of expression quantitative trait loci (Decon-eQTL) into each cell subpopulation.
See DeconCell and Decon-eQTL for their documentation.
The GeneNetwork analysis is a pipeline to predict the gene-pathway scores by using gene expression data. More information can be found in the GeneNetwork analysis wiki page.
PGS-based sample mix-up identification
Idéfix is a novel tool for identifying accidental sample mix-ups in biobanks using polygenic scores. Additional information can be found in the Idéfix wiki page.