GeneExpressionSignature gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.
::DEVELOPER
Yang Cao <yiluheihei at gmail.com>, Fei Li <pittacus at gmail.com>,Lu Han <hanl8910 at gmail.com>
MicroPattern is a tool used to mine regular rules and patterns behind a list of microbes. MicroPattern can also be used to calculate the similarity between the given disease-associated microbe list and the collected micro-disease association dataset
Csbl.go is an R package for computing semantic similarity between genes using Gene Ontology annotation and for clustering genes based on the similarity measures. The package also includes GO enrichment analysis functionality.
TM-score is an algorithm to calculate the similarity of topologies of two protein structures. It can be exploited to quantitatively access the quality of protein structure predictions relative to native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive than root-mean-square deviation (RMSD)
GS-align is a novel computational method for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition, and the optimal alignment is determined by the maximum structural similarity score, GS-score whose significance is size-independent.