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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
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.