COMPARE is an R package with two functions for similarity measurement and clustering. It employs a dynamic programming algorithm to measure spatial similarity between two given datasets. One can then use this function to generate a similarity/affinity matrix which can then be input to the clustering function. The clustering function reports maximal cliques as clusters and dense areas as communities. COMPARE
- is data-size independent
- can effectively circumvent moderate background noise (like batch effect)
- does not need dimension reduction
- does not need subsampling
For more information about its algorithms check out COMPARE-suite's similarity and clustering modules. COMPARE-suite is a pipeline for high-throughput and high-content multiparameter screening built on COMPARE.
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Read the accompanying help page of the package for more details about usage.
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Report any bug/issue on the Issue page.
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