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Gene expression data mining software tools

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MANTEIA
Dataset

MANTEIA

Enables simultaneous comparisons between a wide range of data by combining…

Enables simultaneous comparisons between a wide range of data by combining major resources from human and vertebrate model organisms. Manteia performs several types of analyses as well as data…

BioGPS
Dataset

BioGPS

A centralized gene-annotation portal that enables researchers to access…

A centralized gene-annotation portal that enables researchers to access distributed gene annotation resources. The unique features of BioGPS, compared to those of other gene portals, are its…

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Expression…
Web

Expression Angler

Identifies genes showing similar expression or response profiles from selected…

Identifies genes showing similar expression or response profiles from selected databases. Expression Angler employs the Pearson correlation coefficient to identify co-regulated genes. It provides…

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GEOquery
Desktop

GEOquery

A package that allows access to the wealth of information within GEO directly…

A package that allows access to the wealth of information within GEO directly from BioConductor, eliminating many formatting and parsing problems that have made such analyses labor-intensive in the…

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BrainScope
Web

BrainScope

Enables the linked, all-in-one visualization of genes and samples across the…

Enables the linked, all-in-one visualization of genes and samples across the whole brain and genome, and across developmental stages. BrainScope is a web portal for fast, interactive visual…

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cerebroViz
Desktop

cerebroViz

Maps spatiotemporal brain data to vector graphic diagrams of the human brain.…

Maps spatiotemporal brain data to vector graphic diagrams of the human brain. cerebroViz allows rapid generation of publication-quality figures that highlight spatiotemporal trends in the input data,…

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shinyGEO
Web

shinyGEO

A web application that allows a user to download gene expression data sets…

A web application that allows a user to download gene expression data sets directly from GEO in order to perform differential expression and survival analysis for a gene of interest. In addition,…

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compendiumdb
Desktop

compendiumdb

Provides an environment for downloading functional genomics data from Gene…

Provides an environment for downloading functional genomics data from Gene Expression Omnibus (GEO), parsing the information into a local or remote database, and interacting with the database using…

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GXB
Web
Desktop

GXB Gene Expression Browser

Enables interactive query and navigation of transcriptome datasets relevant to…

Enables interactive query and navigation of transcriptome datasets relevant to human immunology research. GXB can be used to browse context-rich systems-scale data within and across systems…

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MERAV
Web

MERAV Metabolic gEne RApid Visualizer

A web-based tool that can query a database comprising ∼4300 microarrays,…

A web-based tool that can query a database comprising ∼4300 microarrays, representing human gene expression in normal tissues, cancer cell lines and primary tumors. MERAV has been designed as a…

psygenet2r
Desktop

psygenet2r

Allows to retrieve the genes associated to psychiatric diseases. psygenet2r…

Allows to retrieve the genes associated to psychiatric diseases. psygenet2r offers users to study the association between a disease of interest and PsyGeNET diseases based on shared genes. This tool…

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Siamese
Desktop

Siamese

Converts the expression changes of the landmark genes into a perturbation…

Converts the expression changes of the landmark genes into a perturbation barcode that reveals important features of the underlying data. Siamese uses deep learning techniques. The barcode captures…

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D-GEX
Desktop

D-GEX

A deep learning method to infer the expression of target genes from the…

A deep learning method to infer the expression of target genes from the expression of landmark genes. We used the microarray-based GEO dataset, consisting of 111K expression profiles, to train our…

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DGET
Web

DGET Drosophila Gene Expression Tool

Stores and facilitates search of RNA-Seq based expression profiles available…

Stores and facilitates search of RNA-Seq based expression profiles available from the modENCODE consortium and other public data sets. DGET provides a flexible tool for expression data retrieval and…

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LungGENS
Web

LungGENS Lung Gene Expression iN Single-cell

Facilitates the retrieval of lung cell-specific gene expression information…

Facilitates the retrieval of lung cell-specific gene expression information from extensive data sets derived from RNA sequencing of single cells. LungGENS is a web-based bioinformatics resource for…

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LCB
Web

LCB LINCS Canvas Browser

An interactive HTML5 web-based software application that facilitates querying,…

An interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data. LCB implements two compacted layered…

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ARCHS4
Web

ARCHS4 all RNA-seq and ChIP-seq sample and signature search

Provides multiple channels of processed RNA-seq data from GEO/SRA. ARCHS4…

Provides multiple channels of processed RNA-seq data from GEO/SRA. ARCHS4 supports retrospective data analyses and reuse. It can be used to predict gene function and protein-protein interactions.…

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GEOracle
Web
Desktop

GEOracle

Permits to annotate many perturbation experiments from NCBI Gene Expression…

Permits to annotate many perturbation experiments from NCBI Gene Expression Omnibus (GEO) in a semi-automated fashion with full user control. GEOracle follows the same steps a bioinformatcian would…

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ScanGEO
Desktop

ScanGEO

Mines high throughput gene expression data to identify genes and pathways of…

Mines high throughput gene expression data to identify genes and pathways of interest to answer biological questions relevant to diverse fields of study. ScanGEO uses a database query to identify…

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GEMINI
Desktop
Web

GEMINI

A fast search engine that uses a query genomic profile to search for similar…

A fast search engine that uses a query genomic profile to search for similar profiles in a very large genomic database. GEMINI enables users to identify similar profiles independent of sample label,…

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GEO2R
Web

GEO2R

Allows users to compare two or more groups of Samples in a GEO Series in order…

Allows users to compare two or more groups of Samples in a GEO Series in order to identify genes that are differentially expressed across experimental conditions. GEO2R performs comparisons on…

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MARQ
Web

MARQ MicroArray Rank Query

A web-based application that allows researchers to compare a query set of…

A web-based application that allows researchers to compare a query set of genes, e.g. a set of over- and under-expressed genes, against a signature database built from GEO datasets for different…

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BgeeDB
Dataset

BgeeDB

Offers access to reprocessed gene expression datasets from 17 animal species.…

Offers access to reprocessed gene expression datasets from 17 animal species. Bgee aims to compare gene expression patterns across tissues, developmental stages, ages and species. It provides…

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Oncomine
Web

Oncomine

Provides solutions for individual researchers and multinational companies, with…

Provides solutions for individual researchers and multinational companies, with robust, peer-reviewed analysis methods and a powerful set of analysis functions that compute gene expression…

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ProfileChaser
Web

ProfileChaser

A web server that allows for querying the Gene Expression Omnibus based on…

A web server that allows for querying the Gene Expression Omnibus based on genome-wide patterns of differential expression. Using a novel, content-based approach, ProfileChaser retrieves expression…

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GEOmetadb
Desktop
Web

GEOmetadb

Provides an alternative, yet much more flexible and efficient, set of tools for…

Provides an alternative, yet much more flexible and efficient, set of tools for both online and programmatic access to Gene Expression Omnibus (GEO) metadata. GEOmetadb was developed in an attempt to…

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GEM-TREND
Web

GEM-TREND Gene Expression data Mining Toward RElevant Network Discovery

A web tool for searching gene expression data, allows users to search data from…

A web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by…

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tximeta
Desktop

tximeta

Makes numerous annotations and metadata collections. tximeta’ purpose is to…

Makes numerous annotations and metadata collections. tximeta’ purpose is to conserve signature of the transcriptome sequence itself using a hash function.

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E-Northern
Web

E-Northern

Employs annotation of UniGene Expressed Sequence Tag (EST) clusters to retrieve…

Employs annotation of UniGene Expressed Sequence Tag (EST) clusters to retrieve expression data from protein or DNA sequence query.

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GEE
Dataset

GEE Gene Expression data Explore

Compiles information from whole-genome epigenetic and microarray data in public…

Compiles information from whole-genome epigenetic and microarray data in public databases. GEE retrieves suitable high-throughput functional genomic datasets by making specific queries using eVOC and…

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