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Found 57 result(s)

Complete Genomics

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Complete Genomics provides free public access to a variety of whole human genome data sets generated from Complete Genomics’ sequencing service. The research community can explore and familiarize themselves with the quality of these data sets, review the data formats provided from our sequencing service, and augment their own research with additional summaries of genomic variation across a panel of diverse individuals. The quality of these data sets is representative of what a customer can expect to receive for their own samples. This public genome repository comprises genome results from both our Standard Sequencing Service (69 standard, non-diseased samples) and the Cancer Sequencing Service (two matched tumor and normal sample pairs). In March 2013 Complete Genomics was acquired by BGI-Shenzhen , the world’s largest genomics services company. BGI is a company headquartered in Shenzhen, China that provides comprehensive sequencing and bioinformatics services for commercial science, medical, agricultural and environmental applications. Complete Genomics is now focused on building a new generation of high-throughput sequencing technology and developing new and exciting research, clinical and consumer applications.

National Genomics Data Center

国家基因组科学数据中心

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The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), advances life & health sciences by providing open access to a suite of resources, with the aim to translate big data into big discoveries and support worldwide activities in both academia and industry.

JGI MycoCosm

MycoCosm - the fungal genomics resource

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MycoCosm, the DOE JGI’s web-based fungal genomics resource, which integrates fungal genomics data and analytical tools for fungal biologists. It provides navigation through sequenced genomes, genome analysis in context of comparative genomics and genome-centric view. MycoCosm promotes user community participation in data submission, annotation and analysis.

Open Archive for Miscellaneous Data

多元数据归档库

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The Open Archive for Miscellaneous Data (OMIX) database is a data repository developed and maintained by the National Genomics Data Center (NGDC). The database specializes in descriptions of biological studies, including genomic, proteomic, and metabolomic, as well as data that do not fit in the structured archives at other databases in NGDC. It can accept various types of studies described via a simple format and enables researchers to upload supplementary information and link to it from the publication.

Cancer Cell Line Encyclopedia

CCLE

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The Cancer Cell Line Encyclopedia project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

MaizeGDB

Maize Genetics and Genomics Database

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The Maize Genetics and Genomics Database focuses on collecting data related to the crop plant and model organism Zea mays. The project's goals are to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models. MaizeGDB also aims to make the Maize Newsletter available, and provide support services to the community of maize researchers. MaizeGDB is working with the Schnable lab, the Panzea project, The Genome Reference Consortium, and iPlant Collaborative to create a plan for archiving, dessiminating, visualizing, and analyzing diversity data. MMaizeGDB is short for Maize Genetics/Genomics Database. It is a USDA/ARS funded project to integrate the data found in MaizeDB and ZmDB into a single schema, develop an effective interface to access this data, and develop additional tools to make data analysis easier. Our goal in the long term is a true next-generation online maize database.aize genetics and genomics database.

SOL Genomics Network

SGN

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The Sol Genomics Network (SGN) is a clade-oriented database dedicated to the biology of the Solanaceae family which includes a large number of closely related and many agronomically important species such as tomato, potato, tobacco, eggplant, pepper, and the ornamental Petunia hybrida. SGN is part of the International Solanaceae Initiative (SOL), which has the long-term goal of creating a network of resources and information to address key questions in plant adaptation and diversification

FILER: Functional genomics repository

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Harmonized, indexed, searchable large-scale human FG data collection with extensive metadata. Provides scalable, unified way to easily access massive functional genomics (FG) and annotation data collections curated from large-scale genomic studies. Direct integration (API) with custom / high-throughput genetic and genomic analysis workflows.

NCBI Datasets

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NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

Canadian Open Genetics Repository

COGR

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The Canadian Open Genetics Repository is a collaborative effort for the collection, storage, sharing and robust analysis of variants reported by medical diagnostics laboratories across Canada. As clinical laboratories adopt modern genomics technologies, the need for this type of collaborative framework is increasingly important. If you want to join COGR project and get data please send an email at cogr@opengenetics.ca and the introduction to the project will be arranged.

Gemma

Tools and database for meta-analysis of functional genomics data

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Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize co-expression and differential expression results.

Cassavabase

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Breeding, molecular, genetics and genomics data on cassava (Manihot esculenta) and wild relatives

Genome Warehouse

GWH

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The Genome Warehouse (GWH) is a public repository housing genome-scale data for a wide range of species and delivering a series of web services for genome data submission, storage, release and sharing.

Animal QTLdb

Animal Quantitative Trait Loci

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This Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house all publicly available QTL and trait mapping data (i.e. trait and genome location association data; collectively called "QTL data" on this site) on livestock animal species for easily locating and making comparisons within and between species. New database tools are continuely added to align the QTL and association data to other types of genome information, such as annotated genes, RH / SNP markers, and human genome maps. Besides the QTL data from species listed below, the QTLdb is open to house QTL/association date from other animal species where feasible. Note that the JAS along with other journals, now require that new QTL/association data be entered into a QTL database as part of their publication requirements.

NCBI Epigenomics

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>>>!!! <<< The Epigenomics database was retired on June 1, 2016. All epigenomics data are available in our GEO resource https://www.ncbi.nlm.nih.gov/geo >>> !!! <<< The Epigenomics database provides genomics maps of stable and reprogrammable nuclear changes that control gene expression and influence health. Users can browse current epigenomic experiments as well as search, compare and browse samples from multiple biological sources in gene-specific contexts. Many epigenomes contain modifications with histone marks, DNA methylation and chromatin structure activity. NCBI Epigenomics database contains datasets from the NIH Roadmap Epigenomics Project.

megx.net

Marine Ecological GenomiX

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<<<!!!<<< This repository is no longer open to the public !!! >>>!!!>>>

Cancer GenomeAtlas Data Portal

Cancer Genome Atlas Data Portal

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The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The Data Coordinating Center (DCC) is the central provider of TCGA data. The DCC standardizes data formats and validates submitted data.

SoyBase

SoyBase and the Soybean Breeder's Toolbox

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SoyBase is a professionally curated repository for genetics, genomics and related data resources for soybean. It contains current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated "Williams 82" genomic sequence and associated data mining tools. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies.

MicroScope

Microbial Genome Annotation & Analysis Platform

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The MicroScope platform is an informatics infrastructure dedicated to the annotation and comparative analysis of microbial genomes and metagenomes.

Hardwood Genomics Project

HWG

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This database serves forest tree scientists by providing online access to hardwood tree genomic and genetic data, including assembled reference genomes, transcriptomes, and genetic mapping information. The web site also provides access to tools for mining and visualization of these data sets, including BLAST for comparing sequences, Jbrowse for browsing genomes, Apollo for community annotation and Expression Analysis to build gene expression heatmaps.

Plant Genomics and Phenomics Research Data Repository

PGP Repository

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The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and German Plant Phenotyping Network (DPPN) has jointly initiated the Plant Genomics and Phenomics Research Data Repository (PGP) as infrastructure to comprehensively publish plant research data. This covers in particular cross-domain datasets that are not being published in central repositories because of its volume or unsupported data scope, like image collections from plant phenotyping and microscopy, unfinished genomes, genotyping data, visualizations of morphological plant models, data from mass spectrometry as well as software and documents.

TreeGenes

A forest tree genome database

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TreeGenes is a genomic, phenotypic, and environmental data resource for forest tree species. The TreeGenes database and Dendrome project provide custom informatics tools to manage the flood of information.The database contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools. GMOD GUI tools such as CMAP for genetic maps and GBrowse for genome and transcriptome assemblies are implemented here. A sample tracking system, known as the Forest Tree Genetic Stock Center, sits at the forefront of most large-scale projects. Barcode identifiers assigned to the trees during sample collection are maintained in the database to identify an individual through DNA extraction, resequencing, genotyping and phenotyping. DiversiTree, a user-friendly desktop-style interface, queries the TreeGenes database and is designed for bulk retrieval of resequencing data. CartograTree combines geo-referenced individuals with relevant ecological and trait databases in a user-friendly map-based interface. ---- The Conifer Genome Network (CGN) is a virtual nexus for researchers working in conifer genomics. The CGN web site is maintained by the Dendrome Project at the University of California, Davis.

PATRIC

Pathosystems Resource Integration Center

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<<<!!!<<< This repository is no longer available. >>>!!!>>> PATRIC will go offline by mid-December2022. Here is what you need to know. As announced previously, PATRIC, the bacterial BRC, and IRD / ViPR, the viral BRCs, are being merged into the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from these BRCs to provide an integrated resource for bacterial and viral genomics-based infectious disease research.

GigaDB

GigaScience Database

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GigaDB primarily serves as a repository to host data and tools associated with articles published by GigaScience Press; GigaScience and GigaByte (both are online, open-access journals). GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support a unit-of-work (article or study). GigaDB allows the integration of manuscript publication with supporting data and tools.

IHEM Fungi Collection: Human & Animal Health

BCCM/IHEM Fungi Collection: Human & Animal Health

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BCCM/IHEM is a fungal culture collection specialized in medical and veterinary mycology. About 16.000 strains of yeasts and moulds are available from all over the world: pathogens, allergenic species, strains producing mycotoxins, reference strains, teaching material, etc. It also comprises the Raymond Vanbreuseghem collection and the collection of Janssen Pharmaceutica. The BCCM/IHEM collection makes strains or their genomic DNA publicly available for medical, pharmaceutical and biological research, as well as for method validation, testing or educational purposes. Deposits of strains for public access are free of charge for the depositor. The collection also accept safe and patent deposits, and offers a range of services including trainings in mycology and identifications of strains. Moreover, BCCM/IHEM has expertise in fungal taxonomy, in MALDI-TOF MS identification of moulds and yeasts as well as in genomics (whole genome sequencing of fungal strains, phylogenomics, phylogenetics).