subSeq - Subsampling of high-throughput sequencing count data

Subsampling of high throughput sequencing count data for use in experiment design and analysis.

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immunooncologysequencingtranscriptionrnaseqgeneexpressiondifferentialexpression

6.56 score 20 stars 30 scripts 406 downloads

sffdr - Surrogate Functional False Discovery Rates for Genome-Wide Association Studies

Pleiotropy-informed significance analysis of genome-wide association studies with surrogate functional false discovery rates (sfFDR). The sfFDR framework adapts the fFDR to leverage informative data from multiple sets of GWAS summary statistics to increase power in study while accommodating for linkage disequilibrium. sfFDR provides estimates of key FDR quantities in a significance analysis such as the functional local FDR and $q$-value, and uses these estimates to derive a functional $p$-value for type I error rate control and a functional local Bayes' factor for post-GWAS analyses (e.g., fine mapping and colocalization).

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cpp

5.53 score 4 stars 24 scripts 185 downloads

lit - Latent Interaction Testing for Genome-Wide Studies

Identifying latent genetic interactions in genome-wide association studies using the Latent Interaction Testing (LIT) framework. LIT is a flexible kernel-based approach that leverages information across multiple traits to detect latent genetic interactions without specifying or observing the interacting variable (e.g., environment). LIT accepts standard PLINK files as inputs to analyze large genome-wide association studies.

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openblascppopenmp

4.15 score 2 stars 14 scripts 194 downloads