Software Packages & Downloads

Cytoscape

​​​​Cytoscape
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.


NDEx
The NDEx Project provides an open-source framework where scientists and organizations can share, store, manipulate, and publish biological network knowledge on either a free, public website or on private websites.



git-hub-logo


Tutorial for implementing Hannum, et al, MOLCELL 2013. This repository contains all of the analysis notebook required for the reproduction of the manuscript Methylome-wide analysis of chronic HIV infection reveals five-year increase in biological age and epigenetic targeting of HLA.
CliXO


​​​​CliXO
The Clique Extracted Ontologies algorithm (CliXO) infers an ontology in the form of a hierarchical, directed acyclic graph (DAG) from pairwise similarity data. Originally developed for inferring gene ontologies from biological gene networks.


NeXO
NeXO (The Network Extracted Ontology) is a gene ontology inferred directly from large-scale molecular networks. NeXO uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a complete hierarchy of cellular components and processes.​



NBS
Network based stratification (NBS), is a method for stratification (clustering) of patients in a cancer cohort based on genome scale somatic mutations measurements and a gene interaction network.​​




  
Cell Circuit Search
Molecular interaction models provide us with a framework for integrating the large-scale data that we are now able to collect at multiple levels of biological information - genes, RNAs, proteins, and small molecules. Cell Circuit Search is a web-based interface for searching for genes that appear in our library of network models.
NetworkBLAST
NetworkBlast analyzes protein interaction networks in order to predict previously unknown relationships. It can compare multiple species' protein interaction networks and infer interactions through homology. The program is best used in conjunction with Cytoscape to easily visualize the returned data.
PathBLAST
Pathway alignment and query against protein interaction databases to identify conserved protein interaction networks between species. PathBLAST searches the protein-protein interaction network of the target organism to extract all protein interaction pathways that align with a pathway query.
VERA and SAMVERA and SAM
VERA 
and SAM was developed to address the need for a better statistical test for identifying differentially-expressed genes. VERA estimates the parameters of a statistical model that describes multiplicative and additive errors influencing an array experiment, using the method of maximum likelihood. SAM gives a value, lambda, for each gene on an array, which describes how likely it is that the gene is expressed differently between the two cell populations and was developed to address the need for a better statistical test for identifying differentially-expressed genes.
CrazyQuant is a spot-finding tool developed by Trey Ideker while at the University of Washington (cited in O'Reilly's Beginning Perl for Bioinformatics). This JAVA-based applet allows the loading and quantitation of your cDNA microarray images and membranes. 

CrazyQuant is a spot-finding tool developed by Trey Ideker while at the University of Washington (cited in O'Reilly's ). This JAVA-based applet allows the loading and quantitation of your cDNA microarray images and membranes.
Dapple is a program for quantitating spots on a two-color DNA microarray image. Given a pair of images from a comparative hybridization, Dapple finds the individual spots on the image, evaluates their qualities, and quantifies their total fluorescent intensities. Dapple is designed to work with microarrays on glass and is a program for quantitating spots on a two-color DNA microarray image.
Program enoLOGOS generates LOGOs of transcription factor DNA binding sites from various types of input matrices. It can utilize standard count matrices, probability matrices or matrices of "energy" values (i.e., log-frequencies).