A beta-binomial Gaussian process model for ranking features with significant non-random variation in abundance over time. The features are assumed to represent proportions, such as proportion of an alternative allele in a population.
Provides a parametric estimation of genetic effect, enabling straightforward comparison across populations or phenotypes. It provides a middle ground between costly individual-based Genome-Wide Association Studies (GWAS) and two extreme pools contingency test. GWAlpha outperforms contingency tests in most scenarios, unless replicated experiments enable the use of the more powerful Cochran-Mantel-Haenszel test.
A user-friendly application assessing the accuracy of allele frequency estimation from both pool- and individual-based NGS population data under various sampling, sequencing depth and experimental error designs.
Provides an integrated platform for researchers to investigate natural polymorphism and associated functional annotations from UCSC and Flybase genome browsers, population genetic estimators and RNA-seq information.
Permits to analyze pooled DNA data. PDA is based on a four-stage procedure that combines the concept of a three-stage DNA pooling experiment with a procedure of multipoint association test. It permits to estimate allele frequency and allows association testing by directly inputting coefficient of preferential amplification (CPA) values of single nucleotide polymorphisms (SNPs) of interest. The tool is simple to operate and does not require statistical skills.
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