Network Tools

The Kuijjer Group uses the following network tools and resources in their research:

  • PyPanda: Python package for gene regulatory network reconstruction using PANDA (Passing Attributes between Networks for Data Assimilation). 
  • Puma:PANDA Using MicroRNA Associations. PUMA is an extension of PANDA that can include miRNAs are regulators in the regulatory network model. 
  • Lioness:Linear Interpolation to Obtain Network Estimates for Single Samples. LIONESS is an equation that can be used together with network reconstruction algorithms to extract networks for individual samples.
  • netZoo:the network zoo package (by Tian Wang) integrates several network methods, including PANDA (Kimberly Glass), LIONESS, CONDOR (John Platig), and ALPACA (Megha Padi), in one pipeline. 

Other tools

  • SAMBARSubtyping Agglomerated Mutations Using Annotation Relations. SAMBAR de-sparsifies somatic mutation data into pathway mutation scores, and clusters the data into subtypes using binomial distance.
  • YarnYet Another RNA-Seq package (by Joe Paulson). YARN offers robust multi-tissue RNA-Seq preprocessing and normalization.

Learn more about our network tools on our external lab page


Published Oct. 19, 2018 4:50 PM - Last modified Oct. 19, 2018 4:50 PM