:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Dhollander,T. et al. (2007)
Query-driven module discovery in microarray data.
Bioinformatics, 23, 2573-2580.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Sowpati DT, Srivastava S, Dhawan J, Mishra RK.
C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search.
BMC Bioinformatics. 2017 Sep 13;18(Suppl 10):392. doi: 10.1186/s12859-017-1786-6. PMID: 28929968; PMCID: PMC5606219.
:: DESCRIPTION
GMQL provides a next-generation query language for querying NGS data.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
GenoMetric Query Language: A novel approach to large-scale genomic data management.
Masseroli M, Pinoli P, Venco F, Kaitoua A, Jalili V, Palluzzi F, Muller H, Ceri S.
Bioinformatics. 2015 Feb 3. pii: btv048.
:: DESCRIPTION
BGT is a compact file format for efficiently storing and querying whole-genome genotypes of tens to hundreds of thousands of samples.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BGT: efficient and flexible genotype query across many samples.
Li H.
Bioinformatics. 2015 Oct 24. pii: btv613.
:: DESCRIPTION
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
::DEVELOPER
Jack Zhu <zhujack@mail.nih.gov>, Sean Davis @NCI
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2013 Jan 17;14:19. doi: 10.1186/1471-2105-14-19.
SRAdb: query and use public next-generation sequencing data from within R.
Zhu Y, Stephens RM, Meltzer PS, Davis SR.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2018 Dec 1;34(23):4134-4137. doi: 10.1093/bioinformatics/bty447.
MetQy-an R package to query metabolic functions of genes and genomes.
Martinez-Vernon AS, Farrell F, Soyer OS
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
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.
Bioinformatics. 2007 Apr 1;23(7):910-2. Epub 2007 Feb 3.
NetMatch: a Cytoscape plugin for searching biological networks.
Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D.
:: DESCRIPTION
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.
::DEVELOPER
The Integrative Biomedical Informatics group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
The DisGeNET knowledge platform for disease genomics: 2019 update.
Piñero J, Ramírez-Anguita JM, Saüch-Pitarch J, Ronzano F, Centeno E, Sanz F, Furlong LI.
Nucleic Acids Res. 2019 Nov 4. pii: gkz1021. doi: 10.1093/nar/gkz1021.
Anna Bauer-Mehren; Michael Rautschka; Ferran Sanz; Laura I. Furlong:
DisGeNET – a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks.
Bioinformatics, Vol. 26, No. 22. (15 November 2010), pp. 2924-2926.
:: DESCRIPTION
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
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Sep 1;27(17):2451-2. Epub 2011 Jun 27.
CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages.
Bot JJ, Reinders MJ.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sebastian Bauer, Sebastian Köhler, Marcel H. Schulz and Peter N. Robinson
Bayesian Ontology Querying for Accurate and Noise-Tolerant Semantic Searches
Bioinformatics (2012) doi: 10.1093/bioinformatics/b
