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Big data warehousing software tools | Genome annotation

To facilitate the integration and querying of genomics data, a number of generic data warehousing frameworks have been developed. They differ in their design and capabilities, as well as their intended audience. Source text: Triplet and Butler, 2014.

BioMart
Web

BioMart

Integrates BioMart data resources with data analysis software in Bioconductor.…

Integrates BioMart data resources with data analysis software in Bioconductor. BiomaRt can annotate a wide range of gene or gene product identifiers with information such as gene symbol, chromosomal…

Beacon Network
Dataset

Beacon Network

Allows users to share genetic variant data sets collected from large-scale…

Allows users to share genetic variant data sets collected from large-scale population-sequencing projects, clinical diagnostic settings, and variant curation efforts. Beacon Network permits users to…

MAV-seq
Dataset

MAV-seq Management Analysis Visualization of Sequence Data

Facilitates the management of samples metadata and next-generation sequencing…

Facilitates the management of samples metadata and next-generation sequencing (NGS) data pre-processing, quality assessment and visualization. MAV-seq allows to (i) manage research, experiments,…

InterMine
Desktop

InterMine

Provides extensive automatically generated and configurable RESTful web…

Provides extensive automatically generated and configurable RESTful web services. InterMine is especially designed to integrate and analyse complex biological data. It can be used in other…

GOLD
Dataset

GOLD Genomes OnLine Database

A comprehensive online resource to catalog and monitor genetic studies…

A comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated…

modMine
Web

modMine

An integrated web resource of data & tools to browse and search modENCODE…

An integrated web resource of data & tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

TogoWS
Desktop

TogoWS

Provides an integrated interface with advanced features.

Provides an integrated interface with advanced features.

BioWarehouse
Desktop

BioWarehouse

Allows users to compile, handle and mine data. BioWarehouse gathers selected…

Allows users to compile, handle and mine data. BioWarehouse gathers selected databases in a unique database management system using MySQL or Oracle systems. It provides an open-source software…

ACIB PGDB…
Desktop

ACIB PGDB Toolbox

Provides a plug-in for Pathway Tools, an integrated systems biology software to…

Provides a plug-in for Pathway Tools, an integrated systems biology software to create, maintain and query Pathway/Genome Databases (PGDBs). ACIB PGDB Toolbox is fully integrated into the graphical…

GenAp
Desktop

GenAp

A modified version of Spark SQL, a distributed SQL execution engine, that…

A modified version of Spark SQL, a distributed SQL execution engine, that handles efficiently joins that use genomic intervals as keys. With this modification, Spark SQL serves such joins more than…

xGDB
Desktop

xGDB eXtensible Genome Data Broker

Provides a framework for genomic data storage, display and analysis, and offers…

Provides a framework for genomic data storage, display and analysis, and offers integration of existing and novel genome analysis tools. xGBD furnishes a packaged solution to many types of research…

InSilico DB
Web

InSilico DB

A collaborative platform that allows users to share genomic datasets. Dataset…

A collaborative platform that allows users to share genomic datasets. Dataset administrators can add/remove collaborators or groups of collaborators through a dedicated sharing interface. It is…

GtEncseq
Desktop

GtEncseq

Stores multiple biological sequences of variable alphabet size, with…

Stores multiple biological sequences of variable alphabet size, with customizable character transformations, wildcard support, and an assortment of internal representations optimized for different…

AnnotationDbi
Desktop

AnnotationDbi Annotation Database Interface

Provides user interface and database connection code for annotation data…

Provides user interface and database connection code for annotation data packages using SQLite data storage. AnnotationDbi is the virtual base class for all annotation packages. It contains a…

Badger
Desktop
Web

Badger

Provides an easy to use and intuitive way to explore and store genome data and…

Provides an easy to use and intuitive way to explore and store genome data and gene predictions. Badger can be used as a central hub for genome projects allowing project members to search and access…

MicrobeDB
Dataset

MicrobeDB

Provides centralized local storage and access to completed archaeal and…

Provides centralized local storage and access to completed archaeal and bacterial genomes. MicrobeDB creates a simple to use, easy to maintain, centralized local resource for various large-scale…

POS
Web

POS Personalized Oncology Suite

A bioinformatics platform that integrates clinical data, NGS data and…

A bioinformatics platform that integrates clinical data, NGS data and whole-slide bioimages from tissue sections. POS is a web-based platform that is scalable, flexible and expandable. The underlying…

Concierge
Desktop

Concierge

Offers comprehensive support from management of personal digital research…

Offers comprehensive support from management of personal digital research resources to their sharing in open-access neuroinformatics databases. Concierge introduces a desktop application for managing…

Tripal
Desktop

Tripal

Allows construction of online genome databases. Tripal is an open source…

Allows construction of online genome databases. Tripal is an open source toolkit built on the Drupal content management system and that stores data in the recommended standardized biological database…

PanelApp
Web

PanelApp

Permits users to share, download, view and evaluate gene panels. PanalApp aims…

Permits users to share, download, view and evaluate gene panels. PanalApp aims to build a list of genes that can be used to assist diagnose a rare disease. It can be used as a support to identify the…

Sequencing
Dataset

Sequencing

Allows to easily store, use and understand genetic data. Sequencing is a…

Allows to easily store, use and understand genetic data. Sequencing is a collaborative platform that connects app developers that want to build apps with truly personalized, real-time user…

showdb
Desktop

showdb

Display information on configured databases. showdb displays a table with the…

Display information on configured databases. showdb displays a table with the names, contents and access methods of the sequence databases configured for EMBOSS installation. Where the string OK is…

dbtell
Desktop

dbtell

Displays information about a public database. dbtell displays on-screen…

Displays information about a public database. dbtell displays on-screen information on a database with the specific ID. It can write an output file in plain text or HTML containing information.

cacheensembl
Desktop

cacheensembl

Generates server cache file for an Ensembl server. cacheensembl writes a server…

Generates server cache file for an Ensembl server. cacheensembl writes a server cache file which can be saved in the user's “embossdata” directory or, for a system administrator, stored in…

BioXRT
Desktop

BioXRT

Aims to provide a reusable tool for biologists to build online databases…

Aims to provide a reusable tool for biologists to build online databases without in-house development or duplication of effort.

NGS catalog
Dataset

NGS catalog A Database of Next Generation Sequencing Studies in Humans

Compiles information about next generation sequencing (NGS) from published…

Compiles information about next generation sequencing (NGS) from published literature. NGS catalog focuses on curation and management of the available genomic characteristics of disease/trait…

BrassEnsembl
Web

BrassEnsembl

Allows to visualize the 135 k Brassica Exon Array. BrassEnsembl contains 2.4…

Allows to visualize the 135 k Brassica Exon Array. BrassEnsembl contains 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons.…

toxoMine
Dataset

toxoMine data warehouse for Toxoplasma gondii

Provides a powerful interface to support sophisticated integrative exploration…

Provides a powerful interface to support sophisticated integrative exploration of high-throughput data and metadata, providing researchers with a more tractable means toward understanding how genetic…

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