Search Results for "gene" - Page 3

GEAX is a Java application used to visualize and analyze cross-species gene expression microarray data.The program allows comparisons based on fold-change, p-value, quantile matching, or a combination of criteria.

Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE)

Genevar (GENe Expression VARiation) is a platform of database and web services for the integrative analysis and visulization of SNP-gene assocaitaions in eQTL studies.

SAFEGUI is a graphical interface to the safe R package which performs resampling based categorical significance testing for gene expression data.

GEM is a computational method for identification of transcription factor modulators, using expression datasets. The method tests if the correlation between factor and target gene depends on the expression of the modulator.

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74

A new host of CpG Island Explorer 2.0. Original article: An evaluation of new criteria for CpG islands in the human genome as gene markers, Yong Wang on Bioinformatics 2004. http://bioinformatics.oxfordjournals.org/content/20/7/1170.abstract

Moara is a biological text mining tool and consists of a Java library and some auxiliary MySQL databases for gene/protein training and extraction of mentions and its further normalization and disambiguation.

GRaPe - a platform-independent software tool for building integrative gene-reaction-protein (GRP) networks. It generates the kinetic equations for each reaction and outputs a SBML document. It also implements two methods for parameter estimation.

PhenoFam is a web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.

AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general. AnnaF was build upon the pipeline framework Anna.

SLEDRIDE: Simplified Learning about Expression Data Running in a Desktop Environment. To provide a general workbench for pipe-lining microarray gene expression data from supervised learning results into unsupervised learning methods.

Annotare is a tool for annotating Microarray and Gene Expression data. It will help a bench biologist construct a MIAME-compliant MAGE-TAB file.

...Users can combine tools in automatic analysis workflows, which can be shared. Chipster's interactive visualizations allow users to select datapoints and create new gene lists. For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates coverage. Chipster’s ability to provide a biologist-friendly access to a powerful analysis platform is technically based on a desktop application user interface, a flexible distributed architecture, and the ability to integrate many types of analysis tools (command line, R/Bioconductor, Java, Web Services etc). ...

ClutrFree allows the visualization and interpretation of gene expression data clusters for multiple clustering experiments. Data is integrated with ontological annotations (GO), and enrichement of annotations (hypergeometric distribution) is computed.

Genome Data Visualization Toolkit (GDVTK) is a Java library for building bioinformatics visualization application. See Bioinformatics, 2004 Mar 22;20(5):727-34. Java-based application framework for visualization of gene regulatory region annotations.

A simple Java application for the analysis and identification of gene networks. ProPesca takes as input shorts temporal series of realtime-PCR expression levels and it clusters genes that exhibit either similar or specular behaviors.

OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing complex queries against the Gene Ontology Database.

Praxiteles is a cross-platform interactive visualization tool for comparative genome map data. It is particularly well-suited to viewing multiple related genomes or chromosome segments that have highly diverged gene content and order.

The Gene Expression Programming Framework in Java. It separates the process of evolution from the process of interpretation of the chromosome, allowing the use of various schemes in the chromosome.

IGBM (Identification of gene blocks in microorganisms) implements a BLAST-like method to infer conserved gene clusters among closely related prokaryotes, and provides a graphical user interface to navigate the identified clusters and their annotated info

Genome Expression Pathway Analysis Tool - Analysis and Visualization of Microarray Gene Expression Data under Genomic, Proteomic and Metabolic Context

NetAtlas is a Cytoscape plugin that uses tissue gene expression data to filter cellular signaling network. The plugin identifies of tissue-defined networks, tissue-specific network components, and components with correlated expression across tissues.

Application for visualisation of Chromosomal LOcations of Gene Expression.

GSCope3 performs microarray data analysis to find correlations between BLSOM clusters and any form of omic knowledge expressed in OSML. Includes example metabolic pathway, gene ontology, genome position, transcription and PPI knowledge in OSML format.