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Xin He edited this page Sep 21, 2018
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- A generic package for loading/parsing/inmorting/exporting ontology to neo4j.
- A module which deal with annotation data, specifically autism patient data.
- A statistic module for analysis such as enrichment analysis and semantic similarity.
- may contain possible wrapping of existing C++/R/Python code
loading of ontologies files (a) in topOnto and
- Python/Java - pheno4j](https://github.com/phenopolis/pheno4j/tree/master/python)
- Java - SciGraph
- Java - ont4j
- https://arxiv.org/pdf/cmp-lg/9511007.pdf
- https://www.biorxiv.org/content/biorxiv/early/2017/02/16/108977.full.pdf
- https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115692
- (wiki)[https://en.wikipedia.org/wiki/PageRank]
- Colin has python code to export/import obo file to/from the server. NRG is running a neo4j server. (account created:xin)
- Colin: C++ code to construct a network/vetice/edge object.
- Colin: C++ hypergeometric test for enrichment test. Accept the two comparing gene list as input.
- R code for entropy calculation on igraph network. An example in PPI network. The code is currently working with an indirect graph, needs to be implemented to work with a directional graph.
- input should not be restricted to only ontology. Design it to be more generic so that different parser can be implemented to deal with different data, such as patient record, PPI network, etc.