Tools

SEAS

SEAS is a tool to find which clinical (metadata) attributes are enriched within a sample subset.

5/5

PAGER

PAGER is an online systems biology tool for constructing and visualizing gene and PAG networks from multiple PAG genesets.
5/5

HAPPI

HAPPI database is a collection of computer annotated human protein-protein interactions from public data sources and computational predictions.
5/5

DEMA

Distance-bounded Energy-field Minimization Algorithm is a plugin of Cytoscape for data visualization. By generating a layout according to the network information, data analyst can use the layout to perceive the data relations.

5/5

BEERE

BEERE can help biomedical researchers investigate the relevant significance of genes, proteins, and general biomedical concepts—biomedical entities—among one another from public knowledge-base of protein/gene interactions and extracted semantic relationships. 
5/5

WIPER

WIPER tool evaluate all the biomolecular interactions/associations in a network model to generate a rank order of them, based on their in-path traversal scores and a statistical significance test result.
5/5

PGC

This is a technique, which combines the gene expression and the 2D embedded visual information to detect biomarkers from single-cell data.
5/5

WINNER

The code rank the most important genes in a gene lists (seed genes) using their interactions, also expandable to non-seed (expanded) genes.
5/5

DMAP

This database have been developed recently to help with systematic drug repositioning.

5/5

HOMER

This repository defining human organ-specific genes/proteins.

5/5

HIP2

An online database of human plasma proteins from healthy individuals

5/5

ProteoLens

Visual analytic tool for multi-scale database-driven biological network data mining

5/5