SantosJGND/Galaxy_KDE_classifier: Galaxy KDE summary analysis focus

Software for the exploratory analysis of genetic variation across overlapping windows of consecutive markers in large genomics data sets. Feature reduction is combined with kernel density estimation to derive sample-level p-values relative to supervised (reference, user submitted) and unsupervised (MeanShift) local distributions.

This initial layer of analysis is complented with tools to describe the statistics extracted visually (in the form of ideograms) and quantitavely (see /Summary_functions sub-directory). The latter includes scripts for the visual interpretation of summary analyses. Examples from the analysis of variation in the 3,000 Rice Genomes data set are provided.

A small example data set for local execution is provided in the /Simulation_test directory. Main and Ideogram scripts are available through the Galaxy portal.

For more details refer to the readme file in the main directory or contact us directly.

Introducing new summary analysis directories.

• Analysis of variance ratio retained across local windows surveyed. jupyter ready.
• Classification output summary by threshold used. jupyter ready.