Applications & Tools

Network Analysis and Visualization

  1. Arena3Dweb - Interactive 3D visualization of multilayered graphs
  2. NORMA - Apply network layouts based on node groups. 
  3. NAP - Topological network analysis and comparison
  4. VICTOR - Visual analytics for clustering comparison 
  5. SARS-CoV-2 protein proximal interactome - novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms
  6. Viral Infection Network - Host-Virus interaction
  7. HipMCL - Parallel implementation of MCL graph-based clustering
  8. Medusa3 - Visualization of Multi-edge graphs (obsolete)
  9. Human gpDB - Signal transduction / GPCRs-proteins-effectors  (obsolete)

Text-Mining

  1. DARLING - Disease-bioentity associations with literature mining
  2. OnTheFly2.0 - Extract biomedical terms from documents (e.g., docx, pdf)  
  3. EXTRACT - Extract biomedical terms from web pages - (developed by Pafilis and Jensen labs) 
  4. PREGO -  Linking microbes, environments, and processes
  5. UniRed - Protein clustering based on literature
  6. BioTextQuest - Document clustering based on common biomedical terms
  7. BioTextQuesτ v2.0- Document clustering based on common biomedical terms

Genomics/Metagenomics

  1. Flame - Functional enrichment for multiple lists 
  2. MPRAbase - Browse standard MPRA samples
  3. Quadrupia - A database of G-quadruplex sequences and clusters
  4. SCALA - A web application for multimodal analysis of single cell next generation sequencing data 
  5. NMPfamsDB - A database of Novel Metagenome Protein Families
  6. kmerDB - A database encompassing the set of genomic and proteomic sequence information of each species
  7. PASTIS - Extreme-scale many-against-many protein similarity search
  8. Meander - Visualization of genome variations with the use of Hilbert curves 
  9. ProteoSign - Proteomics analysis platform
  10. Human Gene Correlation Analysis (HGCA) - Human gene clustering based on co-expression patterns
  11. Vista-Enhancer Browser - A human and mouse transcriptional enhancer resource, validated in vivo in transgenic mouse embryos.
  12. UHGV - The Unified Human Gut Virome Catalog (UHGV)