This is git repository for the Cytoscape 3 clustering app: clusterMaker

TODO:

1. Fix BiClusterView
2. Add support for BiClustering routines:

• Cheng & Church
• BiMine
• BicFinder

3. New potential cluster algorithms

• CIDR (Lin, Troup, Ho, Genome Biology 2017)
• SPICi (Speed and Performance In Clustering)

7 JUNE - 23 AUGUST 2021 Google Summer of Code by Maija Utriainen

Implementing remote dimensionality reduction techniques using similar approach to last years remote network clusterers (see below).

• Dimensionality reduction techniques added: Isomap, Local Linear Embedding, MDS, Spectral, tSNE, UMAP
• Changes to ClusterJobExecutionService and RemoteServer: abstracting and replacing code to another class
• Subclasses to ClusterJobHandler specific to network clusterers and dimensionality reduction techniques
• The new algorithms registered in CyActivator

The added and edited code can be found in clusterMaker2/src/main/java/edu/ucsf/rbvi/clusterMaker2/internal/

• utils/remoteUtils
  • RemoteServer
  • ClusterJobExecutionService
  • NetworkClusterJobHandler
  • DimensionalityReductionJobHandler
• algorithms/dimensionalityRedcution
  • isomap
  • linearEmbedding
  • mds
  • spectral
  • tSNERemote
  • umap
• CyActivator

1 JUNE - 29 AUGUST 2020 changes done as a Google Summer of Code Project by Maija Utriainen

Implementing new algorithms with a new approach that runs the algorithm remotely on a server instead of in clusterMaker/Cytoscape utilizing interfaces in cytoscape.jobs package.

• The algorithms: Leiden, Infomap, Fast Greedy, Leading Eigenvector, Label Propagation, Multilevel
• The classes used to carry out the remote clustering job are found in remoteUtils. Most of these classes are extended from cytoscape.jobs interfaces and classes and are: ClusterJob, ClusterJobData, ClusterJobDataService, ClusterJobExecutionService, ClusterJobHandler and RemoteServer.
• The algorithms and ClusterJobExecutionService registered in CyActivator.

My code can be found in several packages in clusterMaker2/src/main/java/edu/ucsf/rbvi/clusterMaker2/internal/

• utils/remoteUtils
• algorithms/networkClusterers
  • Leiden
  • Infomap
  • FastGreedy
  • LeadingEigenVector
  • LabelPropagation
  • Multilevel
• CyActivator