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