QDB (Query Driven Biclustering) is a Bayesian query-driven biclustering framework for microarray data in which the prior distributions allow introducing knowledge from a set of seed genes (query) to guide the pattern search.
C-State (Chromatin-State) is an interactive platform that enables experimentalists who lack bioinformatics support to investigate epigenetic landscapes across multiple datasets for comparative epigenomic analysis.
SRAdb is an attempt to make queries of the metadata associated with SRA (Sequence Read Archive ) submission, study, sample, experiment and run more robust and precise, and make access to sequencing data in the SRA easier
MetQy (metabolic query) is a R package to ease interfacing with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to query metabolic functions of genes and genomes.
NetMatch* is a Cytoscape app that allow user to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. NetMatch* also allows queries with wildcards.
Version 2. F1000Res. 2015 Aug 5 [revised 2015 Nov 3];4:479. doi: 10.12688/f1000research.6656.2. eCollection 2015. NetMatchStar: an enhanced Cytoscape network querying app.
Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A, Giugno R.
DisGeNET is a plugin for Cytoscape to query and analyze a network representation of human gene-disease databases. For this purpose, we have developed a new gene-disease database integrating data from several public sources. DisGeNET allows user-friendly access to our database, which includes queries restricted to (i) the original data source, (ii) the association type, (iii) the disorder class of interest and (iv) specific diseases, respectively genes. It represents gene-disease associations in terms of bipartite graphs and additionally provides gene centric and disease centric views of the data. It assists the user in the interpretation and exploration of human complex diseases with respect to their genetic origin by a variety of built-in functions. Moreover, DisGeNET permits multicoloring of nodes (genes/diseases) according to their disease classes for expedient visualization
DisGeNET2R contains a series of functions to retrieve and expand gene-disease, and variant-disease data, and to perform mappings of several biomedical vocabularies.
CytoscapeRPC is a Cytoscape plug-in which allows users to create, query and modify Cytoscape networks. This means that you can automate your Cytoscape tasks from any programming language which supports XML-RPC
BOQA integrates the knowledge stored in an ontology and the accompanying annotations into a Bayesian network in order to implement a search system in which users enter one or more terms of the ontology to get a list of appropriate domain items.