CORE - Cores of Recurrent Events
Given a collection of intervals with integer start and end positions, find recurrently targeted regions and estimate the significance of finding. Randomization is implemented by parallel methods, either using local host machines, or submitting grid engine jobs.
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3.53 score 337 scripts 225 downloadsCNprep - Pre-Process DNA Copy Number (CN) Data for Detection of CN Events
DNA copy number data evaluation using both their initial form (copy number as a noisy function of genomic position) and their approximation by a piecewise-constant function (segmentation), for the purpose of identifying genomic regions where the copy number differs from the norm.
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1.48 score 30 scripts 210 downloadsTBEST - Tree Branches Evaluated Statistically for Tightness
Our method introduces mathematically well-defined measures for tightness of branches in a hierarchical tree. Statistical significance of the findings is determined, for all branches of the tree, by performing permutation tests, optionally with generalized Pareto p-value estimation.
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1.30 score 8 scripts 207 downloads