HTSanalyzeR2

This package provides gene set over-representation, gene set enrichment analysis and enriched subnetwork analyses. 🚀


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Tutorials

Porvide 3 case study for reference

This case study uses HTSanalyzeR2 to perform gene set over-representation analysis, enrichment analysis and enriched subnetwork analyses on a common gene expression profile.

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This case study uses a time series CRISPR genome-wide drop-out data as a demonstration to perform time series analysis.

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In case if you only have a list of genes and want to do hypergeometric test with gene sets having known functions

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Resources

Contains the preprocessing, Hypergeometrics, Enrichment Subnetwork

Preprocessing

a preprocess step including invalid input data removing, duplication removing, initial gene identifiers converting to Entrez ID and phenotype ordering.

Hypergeometric test

This part will briefly introduce Hypergeometric Distribution and the test.

Enriched subnetwork analysis

You can also perform subnetwork analysis (Beisser (2010), Dittrich MT (2008)) to extract the subnetwork enriched with nodes which are associated with a significant phenotype using HTSanalyzeR2.

Contact us

Please contact to Correcting error and/or Giving advices. Thanks!

  • linqi23-c@my.cityu.edu.hk
  • Dr.Xin Wang's Lab.
    Room 315, Block 2, To Yuen Building, City University of Hong Kong, Hong Kong
  • 10:00 to 17:00 on workdays