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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 coordinates, Gene Ontology and Online Mendelian Inheritance in Man (OMIM) annotation. Furthermore, biomaRt enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. Fast and up-to-date data retrieval is possible as the package executes direct SQL queries to the BioMart databases. The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining.
xGDB / eXtensible Genome Data Broker
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 applications. In particular, it is well suited for small to moderately sized research groups desiring local access to genomic data or an out-of-the-box system for analyzing emerging data. xGDB differs from and is complementary to database systems such as GMOD, EnsEMBL, and GenBank.
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 schema, Chado. This software consists of a core set of modules that encompass a variety of common biological and genetic data types, such as organisms, sequence features and genetic markers which include attributes such as genus and species, nucleotide residues and marker locations, respectively.
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 user interface (GUI) and menu. It extends the application’s functionality by the ability to create multiple sequence alignments, systematically annotate insertion sequence (IS) elements and analyse their activity by cross-species comparison tools. Microarray probes can be automatically mapped to target genes, and expression data obtained with these arrays can be transformed into input formats needed to visualize them in the various omics viewers of Pathway Tools. The plug-in API itself allows developers to integrate their own functions into the Pathway Tools menu.
AnnotationDbi / Annotation Database Interface
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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 database connection and is meant to be the parent for a set of classes in the Bioconductor annotation packages. The package includes: organism, platform, homology and system-biology.
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 personal digital research resources. The metadata stored in this application can also be uploaded (together with the primary resource) to neuroinformatics databases without additional efforts. This interaction between personal and shared neuroinformatics databases is expected to enhance digital research resource circulation.
Bio-SeCo / Bioinformatics Search Computing application
Allows searching, exploration and ranking-aware combination of distributed bio-data. Bio-SeCo is an application that enables explorative search and automatic ranking-aware integration of heterogeneous biomedical-molecular data provided by the individual services registered in the framework. The registered services, in the user interface, can be used and combined, according to their connection patterns defined at service registration time, to explore and globally search the data that they provide.
Stores multiple biological sequences of variable alphabet size, with customizable character transformations, wildcard support, and an assortment of internal representations optimized for different distributions of wildcards and sequence lengths. GtEncseq offers a flexible and easily configurable alphabet transformation which is useful for many applications. It offers unique features like accessing the same sequence using different reading directions and access to a sequence virtually concatenated with its reverse complement.
VecNet-DW / Vector-Borne Disease Network Data Warehouse
Allows storage, accession, and analysis of malaria-related data scattered in heterogeneous forms across many data storage systems. VecNet-DW provides online analytical processing (OLAP) functionalities such as slice and dice, roll up and roll down. It permits users to browse, aggregate, and download portions of VecNet-DW content for offline analysis. This tool offers a multidimensional cube view of data that promotes understandability by allowing data visualization.
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 given next to a database listed in showdb output, this means showdb has read the database definition correctly and that this access method is in principle possible, in other words, the database has been configured correctly. It does not mean that the database or access method are available or working correctly.
InSilico DB
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 possible, as discussed in the 'Grouping and sub-grouping' section to create a new dataset by grouping samples from independent datasets. These newly generated datasets are private by default - that is, only the owner has access to them. Sharing preferences and the public status of the dataset can be changed by the owner. An owner of a dataset can make it public to the InSilico DB community or keep it private. A private dataset can be shared with collaborators who can be given read-only or read-and-write permissions. A user who has read-and-write permissions on a dataset can edit its sharing preferences.
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Beacon Network
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 choose from a predetermined set of conditions that restrict potential data use on the basis of the consent of individuals represented in the data. It overcomes the inefficiency and expense experienced when data generators must transfer whole copies of their data sets into a single, centralized repository.
MAV-seq / Management Analysis Visualization of Sequence Data
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, samples and NGS metadata; (ii) control access to the centralized and distributed storage and high-performance computing resources; (iii) automate and standardize quality checking, pre-processing and analysis of NGS data with visualization and report generation of obtained results.
toxoMine / data warehouse for Toxoplasma gondii
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 and/or epigenetic factors play a coordinated role in determining the pathogenicity of Toxoplasma gondii. It comes with a user-friendly web interface and powerful tools that give users the capability and flexibility to explore and interrogate data and metadata available using a number of different approaches.
Allows organization of data from individual databases into one query-optimized system, using a data warehousing technique specifically designed for descriptive data. EnsMart is based on the principle of creating a generic system from specific data sources, where disparate data can be integrated and interrogated in a flexible, unified, and domain-independent manner. The database provides scalability for large amounts of data, support for integration with third-party data and/or programs, and user interfaces. The solution can be adapted to any database containing descriptive data.
NGS catalog / A Database of Next Generation Sequencing Studies in Humans
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 associated to single nucleotide variants (SNVs), small indels, copy number variations (CNVs), and large structural variants (SVs). It also collects mutated genes and their variants and gene fusions detected by NGS technologies if such information can be obtained from the literature.
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