Zelakolase / TrSC

TrSC

Top-ranked Selective Clustering, Protein-Protein Interaction Network Usecase

• TrSC
  • Class list (in src/)
  • Indicators
  • Build and Run
  • License
  • Available datasets

Class list (in src/)

• algorithms/
  • Clustering : TrSC clustering algorithm (inc. ranking eq.)
  • Stats : Calculation of Graph Completeness Ratio, Ratio of Connectivity, Mean, Standard Deviation
  • GPI : Calculation of General Performance Indicator
• lib/
  • GORead : Reads STRING-DB short TSV file to Graph object
  • Graph : Weighted undirected graph object (data structure + CRUD functions)
  • IO : Disk IO r/w
  • SparkDB : Check NaDeSys/SparkDB repository
• App : Make a ranked table comparing the mean GCR, mean-stdev GCR, mean RC, mean-stdev RC, num. clusters, GPI, and mean cluster size for MCL, Louvain, CliXO, infomap, and TrSC for all of the available dataset.
• SingleGO : Makes a report on TrSC clustering for a specified GO term in dataset.

Indicators

• Graph Completeness Ratio (GCR): SumWeights divided by SumMaxWeights.
• Ratio of Connectivity (RC) : Num.Edges divided by Max.Num.Edges.
• General Performance Indicator (GPI) : Merges GCR and RC values to a single scalar.

Build and Run

The current runnable classes are App and SingleGO $ cd src/; chmod +x buildAndRun.sh; ./buildAndRun.sh [classname]

License

Top-ranked Selective Clustering Algorithm © 2023 by Morad A.; Norhan A.K. is licensed under Attribution-ShareAlike 4.0 International. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/

Available datasets

All GO terms under GO:0008150 (Biological Process) under 2,000 homosapien proteins:

• GO:0000003 (Reproduction)
• GO:0016032 (Viral Process)
• GO:0022414 (Reproductive Process)
• GO:0040007 (Growth)
• GO:0040011 (Locomotion)
• GO:0042592 (Homeostatic Process)
• GO:0043473 (Pigmentation)
• GO:0098754 (Detoxification)

Note: ALS.tsv is related to a test case.