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bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
The Human Sleep Project (HSP) sleep physiology dataset is a growing collection of clinical polysomnography (PSG) recordings. Beginning with PSG recordings from from ~15K patients evaluated at the Massachusetts General Hospital, the HSP will grow over the coming years to include data from >200K patients, as well as people evaluated outside of the clinical setting. This data is being used to develop CAISR (Complete AI Sleep Report), a collection of deep neural networks, rule-based algorithms, and signal processing approaches designed to provide better-than-human detection of conventional PSG...
bambioinformaticsbiologycramgeneticgenomicgenotypinglife sciencesmachine learningpopulation geneticsshort read sequencingstructural variationtertiary analysisvariant annotationwhole genome sequencing
This dataset contains alignment files and short nucleotide, copy number (CNV), repeat expansion (STR), structural variant (SV) and other variant call files from the 1000 Genomes Project Phase 3 dataset (n=3202) using Illumina DRAGEN v3.5.7b, v3.7.6, v4.0.3, and v4.2.7 software. All DRAGEN analyses were performed in the cloud using the Illumina Connected Analytics bioinformatics platform powered by Amazon Web Services (see 'Data solution empowering population genomics' for more information). The v3.7.6 and v4.2.7 datasets include results from trio small variant, de novo structural vari...
bioinformaticscell biologylife sciencessingle-cell transcriptomicstranscriptomics
CZ CELLxGENE Discover (cellxgene.cziscience.com) is a free-to-use platform for the exploration, analysis, and retrieval of single-cell data. CZ CELLxGENE Discover hosts the largest aggregation of standardized single-cell data from the major human and mouse tissues, with modalities that include gene expression, chromatin accessibility, DNA methylation, and spatial transcriptomics. This year, CZ CELLxGENE Discover has made available all of its human and mouse RNA single-cell data through Census (https://chanzuckerberg.github.io/cellxgene-census/) – a free-to-use service with an API and data that...
bioinformaticsbiologycancercell biologycell imagingcell paintingchemical biologycomputer visioncsvdeep learningfluorescence imaginggenetichigh-throughput imagingimage processingimage-based profilingimaginglife sciencesmachine learningmedicinemicroscopyorganelle
The Cell Painting Gallery is a collection of image datasets created using the Cell Painting assay. The images of cells are captured by microscopy imaging, and reveal the response of various labeled cell components to whatever treatments are tested, which can include genetic perturbations, chemicals or drugs, or different cell types. The datasets can be used for diverse applications in basic biology and pharmaceutical research, such as identifying disease-associated phenotypes, understanding disease mechanisms, and predicting a drug’s activity, toxicity, or mechanism of action (Chandrasekaran et al 2020). This collection is maintained by the Carpenter–Singh lab and the Cimini lab at the Broad Institute. A human-friendly listing of datasets, instructions for accessing them, and other documentation is at the corresponding GitHub page abou...
bioinformaticsgeneticgenomiclife sciencespopulationpopulation geneticsshort read sequencingwhole genome sequencing
The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators that aggregates and harmonizes both exome and genome data from a wide range of large-scale human sequencing projects. The summary data provided here are released for the benefit of the wider scientific community without restriction on use. The v4.1 data set (GRCh38) spans 730,947 exome sequences and 76,215 whole-genome sequences from unrelated individuals, of diverse ancestries, sequenced sequenced as part of various disease-specific and population genetic studies. The gnomAD Principal Investigators and team can be found here, and the groups that have contributed data to the current release are listed here. Sign up for the gnom...
bambioinformaticsfast5fastafastqgenomiclife scienceslong read sequencingshort read sequencingtranscriptomics
The Singapore Nanopore Expression (SG-NEx) project is an international collaboration to generate reference transcriptomes and a comprehensive benchmark data set for long read Nanopore RNA-Seq. Transcriptome profiling is done using PCR-cDNA sequencing (PCR-cDNA), amplification-free cDNA sequencing (direct cDNA), direct sequencing of native RNA (direct RNA), and short read RNA-Seq. The SG-NEx core data includes 5 of the most commonly used cell lines and it is extended with additional cell lines and samples that cover a broad range of human tissues. All core samples are sequenced with at least 3 ...
bioinformaticsgenomiclife scienceslong read sequencing
The dataset contains reference samples that will be useful for benchmarking and comparing bioinformatics tools for genome analysis. Examples include: NA12878 (HG001) and NA24385 (HG002) sequenced on an Oxford Nanopore Technologies (ONT) PromethION using the latest R10.4.1 flowcells; and, UHR RNA (direct-RNA) on an ONT PromethION using the latest RNA004 flowcells. Raw signal data output by the sequencer is provided for these datasets in BLOW5 format, and can be rebasecalled when basecalling software updates bring accuracy and feature improvements over the years. Raw signal data is not only for ...
bambioinformaticsbiologycoronavirusCOVID-19fast5fastafastqgeneticgenomichealthjsonlife scienceslong read sequencingmedicineMERSmetadataopen source softwareRDFSARSSARS-CoV-2SPARQL
COVID-19 PubSeq is a free and open online bioinformatics public sequence resource with on-the-fly analysis of sequenced SARS-CoV-2 samples that allows for a quick turnaround in identification of new virus strains. PubSeq allows anyone to upload sequence material in the form of FASTA or FASTQ files with accompanying metadata through the web interface or REST API.
bioinformaticsbiologyenvironmentalepigenomicsgeneticgenomiclife sciences
The TaRGET (Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription) Program is a research consortium funded by the National Institute of Environmental Health Sciences (NIEHS). The goal of the collaboration is to address the role of environmental exposures in disease pathogenesis as a function of epigenome perturbation, including understanding the environmental control of epigenetic mechanisms and assessing the utility of surrogate tissue analysis in mouse models of disease-relevant environmental exposures.
bioinformaticsbiologygeneticgenomiclife sciencesreference index
This dataset provides genomic reference data and software packages for use with Galaxy and Bioconductor applications. The reference data is available for hundreds of reference genomes and has been formatted for use with a variety of tools. The available configuration files make this data easily incorporable with a local Galaxy server without additional data preparation. Additionally, Bioconductor's AnnotationHub and ExperimentHub data are provided for use via R packag...
bambioinformaticsbiologyCaenorhabditis elegansfastqgatk-svgenetic mapsgenomegenome wide association studygenomiclife sciencesshort read sequencingvariant annotationvcf
The Caenorhabditis Natural Diversity Resource (CaeNDR) is a data repository and analysis hub of wild strains of selfing Caenhorabditis species C. elegans, C. briggsae, and C. tropicalis from around the world to facilitate discovery of genetic variation across all three species through genome-wide association mappings to correlate genotype with phenotype and identify genetic variation underlying quantitative traits.
bioinformaticsbiologygeneticgenomichealthlife sciencesproteinreference indextranscriptomics
A centralized repository of pre-formatted BLAST databases created by the National Center for Biotechnology Information (NCBI).
bioinformaticsbiologygeneticgenomiclife sciences
The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. ENCODE investigators employ a variety of assays and methods to identify functional elements. The discovery and annotation of gene elements is accomplished primarily by sequencing a ...
bioinformaticsbiologygeneticgenomicinfrastructurelife sciencessingle-cell transcriptomicstranscriptomicswhole genome sequencing
Pre-built refgenie reference genome data assets used for aligning and analyzing DNA sequence data.
bioinformaticshealthlife sciencesnatural language processingus
The Synthea generated data is provided here as a 1,000 person (1k), 100,000 person (100k), and 2,800,000 persom (2.8m) data sets in the OMOP Common Data Model format. SyntheaTM is a synthetic patient generator that models the medical history of synthetic patients. Our mission is to output high-quality synthetic, realistic but not real, patient data and associated health records covering every aspect of healthcare. The resulting data is free from cost, privacy, and security restrictions. It can be used without restriction for a variety of secondary uses in academia, research, industry, and gov...
bioinformaticsbiologycancergeneticgenomicHomo sapienslife sciencesreference index
Broad maintained human genome reference builds hg19/hg38 and decoy references.
bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
The International Cardiac Arrest REsearch consortium (I-CARE) Database includes baseline clinical information and continuous electroencephalography (EEG) recordings from 1,020 comatose patients with a diagnosis of cardiac arrest who were admitted to an intensive care unit from seven academic hospitals in the U.S. and Europe. Patients were monitored with 18 bipolar EEG channels over hours to days for the diagnosis of seizures and for neurological prognostication. Long-term neurological function was determined using the Cerebral Performance Category scale.
benchmarkbioinformaticslife sciencesmetagenomicsmicrobiome
Database for use with Kraken2 (taxonomic annotation of metagenomic sequencing reads) including all NCBI RefSeq genomes available in release V205
bioinformaticshealthlife sciencesnatural language processingus
MIMIC-III (‘Medical Information Mart for Intensive Care’) is a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital. Data includes vital signs, medications, laboratory measurements, observations and notes charted by care providers, fluid balance, procedure codes, diagnostic codes, imaging reports, hospital length of stay, survival data, and more. The database supports applications including academic and industrial research, quality improvement initiatives, and higher education coursework. The MIMIC-I...
bioinformaticsbiologyGeneLabgenomicimaginglife sciencesspace biology
NASA’s Space Biology Open Science Data Repository (OSDR) introduces a one-stop site where users can explore and contribute a variety of NASA open science biological data. This site consolidates data from the Ames Life Sciences Data Archive (ALSDA) and GeneLab and includes information about the broader NASA Open Science and Open Data initiatives, all at one centralized location. Our mission is to maximize the utilization of the valuable biological research resources and enable new discoveries.
OSDR introduces access to data generated from spaceflight and space relevant experiments that explore ...
bioinformaticsbiologyecosystemsenvironmentalgeneticgenomichealthlife sciencesmetagenomicsmicrobiome
QIIME 2 (pronounced “chime two”) is a microbiome multi-omics bioinformatics and data science platform that is trusted, free, open source, extensible, and community developed and supported.
bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
The IIIC dataset includes 50,697 labeled EEG samples from 2,711 patients' and 6,095 EEGs that were annotated by physician experts from 18 institutions. These samples were used to train SPaRCNet (Seizures, Periodic and Rhythmic Continuum patterns Deep Neural Network), a computer program that classifies IIIC events with an accuracy matching clinical experts.
bioinformaticslife sciencesmedicinepharmaceuticalstructural biology
VirtualFlow Versions of Ligand Libraries in Ready-To-Dock Format
bioinformaticsbiologygeneticgenomicimaginglife sciences
The goal of the National Institutes of Health (NIH) Common Fund’s 4D Nucleome (4DN) program is to study the three-dimensional organization of the nucleus in space and time (the 4th dimension). The nucleus of a cell contains DNA, the genetic “blueprint” that encodes all of the genes a living organism uses to produce proteins needed to carry out life-sustaining cellular functions. Understanding the conformation of the nuclear DNA and how it is maintained or changes in response to environmental and cellular cues over time will provide insights into basic biology as well as aspects of human health...
biodiversitybioinformaticslife sciences
The Biodiversity Heritage Library (BHL) is the world’s largest open access digital library for biodiversity literature and archives. BHL operates as a worldwide consortium of natural history, botanical, research, and national libraries working together to digitize the natural history literature held in their collections and make it freely available for open access.
amazon.sciencebioinformaticsbiologycoronavirusCOVID-19healthlife sciencesmedicineMERSSARS
A centralized repository of up-to-date and curated datasets on or related to the spread and characteristics of the novel corona virus (SARS-CoV-2) and its associated illness, COVID-19. Globally, there are several efforts underway to gather this data, and we are working with partners to make this crucial data freely available and keep it up-to-date. Hosted on the AWS cloud, we have seeded our curated data lake with COVID-19 case tracking data from Johns Hopkins and The New York Times, hospital bed availability from Definitive Healthcare, and over 45,000 research articles about COVID-19 and rela...
bioinformaticsbiologygenomiclife sciencesmappingmedicinereference indexwhole genome sequencing
Genomic tools use reference databases as indexes to operate quickly and efficiently, analogous to how web search engines use indexes for fast querying. Here, we aggregate genomic, pan-genomic and metagenomic indexes for analysis of sequencing data.
bambioinformaticscoronavirusCOVID-19fastafastqgeneticgenomicglobalhealthlife scienceslong read sequencingSARS-CoV-2vcfviruswhole genome sequencing
The Sequence Read Archive (SRA) is the primary archive of high-throughput sequencing data, hosted by the National Institutes of Health (NIH). The SRA represents the largest publicly available repository of SARS-CoV-2 sequencing data. This dataset was created by DNAstack using SARS-CoV-2 sequencing data sourced from the SRA. Where possible, raw sequence data were processed by DNAstack through a unified bioinformatics pipeline to produce genome assemblies and variant calls. The use of a standardized workflow to produce this harmonized dataset allows public data generated using different methodol...
bioinformaticsbiologycomputer visioncsvhealthimaginglabeledlife sciencesmachine learningmedical image computingmedical imagingradiologyx-ray
The Emory Knee Radiograph (MRKR) dataset is a large, demographically diverse collection of 503,261 knee radiographs from 83,011 patients, 40% of which are African American. This dataset provides imaging data in DICOM format along with detailed clinical information, including patient- reported pain scores, diagnostic codes, and procedural codes, which are not commonly available in similar datasets. The MRKR dataset also features imaging metadata such as image laterality, view type, and presence of hardware, enhancing its value for research and model development. MRKR addresses significant gaps ...
bioinformaticsbiologycromwellgatk-svgeneticgenomiclife sciencesstructural variation
This dataset holds the data needed to run a structural variation discovery pipeline for Illumina short-read whole-genome sequencing (WGS) data in AWS.
bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
The Harvard EEG Database will encompass data gathered from four hospitals affiliated with Harvard University:Massachusetts General Hospital (MGH), Brigham and Women's Hospital (BWH), Beth Israel Deaconess Medical Center (BIDMC), and Boston Children's Hospital (BCH).
bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
The Harvard-Emory ECG database (HEEDB) is a large collection of 12-lead electrocardiography (ECG) recordings, prepared through a collaboration between Harvard University and Emory University investigators.
bioinformaticsgeneticgenomiclife sciencesmetagenomicsviruswhole genome sequencing
Preprocessed databases for use with the Hecatomb pipeline for viral and phage sequence annotation.
bioinformaticsbiologygenomiclife sciencesmetagenomicsmicrobiomereference indexwhole genome sequencing
This dataset comprises pre-built indexes for the bioinformatics software Kaiju, which is used for taxonomic classification of metagenomic sequencing data. Various indexes for different source reference databases are available.
amino acidarchivesbioinformaticsbiomolecular modelingcell biologychemical biologyCOVID-19electron microscopyelectron tomographyenzymelife sciencesmoleculenuclear magnetic resonancepharmaceuticalproteinprotein templateSARS-CoV-2structural biologyx-ray crystallography
The "Protein Data Bank (PDB) archive" was established in 1971 as the first open-access digital data archive in biology. It is a collection of three-dimensional (3D) atomic-level structures of biological macromolecules (i.e., proteins, DNA, and RNA) and their complexes with one another and various small-molecule ligands (e.g., US FDA approved drugs, enzyme co-factors). For each PDB entry (unique identifier: 1abc or PDB_0000001abc) multiple data files contain information about the 3D atomic coordinates, sequences of biological macromolecules, information about any small molecules/ligan...
bioinformaticsbiologychemistryenzymegraphlife sciencesmoleculeproteinRDFSPARQL
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt consortium and host institutions EMBL-EBI, SIB Swiss Institute of Bioinformatics and PIR are committed to the long-term preservation of the UniProt databases.
amazon.sciencebioinformaticshealthlife sciencesnatural language processingus
DE-SynPUF is provided here as a 1,000 person (1k), 100,000 person (100k), and 2,300,000 persom (2.3m) data sets in the OMOP Common Data Model format. The DE-SynPUF was created with the goal of providing a realistic set of claims data in the public domain while providing the very highest degree of protection to the Medicare beneficiaries’ protected health information. The purposes of the DE-SynPUF are to:
bambioinformaticsbiologycoronavirusCOVID-19cramfastqgeneticgenomichealthlife sciencesMERSSARSSTRIDEStranscriptomicsviruswhole genome sequencing
This repository within the ACTIV TRACE initiative houses a comprehensive collection of datasets related to SARS-CoV-2. The processing of SARS-CoV-2 Sequence Read Archive (SRA) files has been optimized to identify genetic variations in viral samples. This information is then presented in the Variant Call Format (VCF). Each VCF file corresponds to the SRA parent-run's accession ID. Additionally, the data is available in the parquet format, making it easier to search and filter using the Amazon Athena Service. The SARS-CoV-2 Variant Calling Pipeline is designed to handle new data every six ho...
amino acidbioinformaticsbiomolecular modelinglife sciencesmolecular dynamicsproteinstructural biology
Co-managed by Toyoko and the Structural Biology Group at the Universidad Nacional de Quilmes, this dataset allows us to explore the conformational space of all possible peptides using the 20 common amino acids. It consists of a collection of exhaustive molecular dynamics simulations of tripeptides and pentapeptides.
bioinformaticsbiologycancergeneticgenomiclife sciences
The GATK test data resource bundle is a collection of files for resequencing human genomic data with the Broad Institute's Genome Analysis Toolkit (GATK).
biodiversitybioinformaticsconservationearth observationlife sciences
The Global Biodiversity Information Facility (GBIF) is an international network and data infrastructure funded by the world's governments providing global data that document the occurrence of species. GBIF currently integrates datasets documenting over 1.6 billion species occurrences, growing daily. The GBIF occurrence dataset combines data from a wide array of sources including specimen-related data from natural history museums, observations from citizen science networks and environment recording schemes. While these data are constantly changing at GBIF.org, periodic snapshots are taken a...
bioinformaticsbiologyfast5fastqgenomicHomo sapienslife scienceswhole genome sequencing
The ont-open-data registry provides reference sequencing data from Oxford Nanopore Technologies to support, 1) Exploration of the characteristics of nanopore sequence data. 2) Assessment and reproduction of performance benchmarks 3) Development of tools and methods. The data deposited showcases DNA sequences from a representative subset of sequencing chemistries. The datasets correspond to publicly-available reference samples (e.g. Genome In A Bottle reference cell lines). Raw data are provided with metadata and scripts to describe sample and data provenance.
bioinformaticscsvdicomgenomichealthimaginglife sciencesmedicine
This is a synthetic data set that includes FHIR resources, DICOM images, genomic data, physiological data (i.e., ECGs), and simple clinical notes. FHIR links all the data types together.
bioinformaticsbiologycancercsvgene expressiongeneticgenomicHomo sapienslife sciencesMus musculusneurosciencetranscriptomics
recount3 is an online resource consisting of RNA-seq gene, exon, and exon-exon junction counts as well as coverage bigWig files for 8,679 and 10,088 different studies for human and mouse respectively. It is the third generation of the ReCount project and part of recount.bio. recount2 is also included for historical purposes. The pipeline used to generate the data in recount3 (but not recount2) is available here.
bioinformaticsbiologycoronavirusCOVID-19life sciencesmolecular dockingpharmaceutical
Aggregating critical information to accelerate drug discovery for the molecular modeling and simulation community. A community-driven data repository and curation service for molecular structures, models, therapeutics, and simulations related to computational research related to therapeutic opportunities for COVID-19 (caused by the SARS-CoV-2 coronavirus).
assemblybioinformaticsbiologycontaminationfastageneticgenomehealthlife scienceswhole genome sequencing
Sequence database used by FCS-GX (Foreign Contamination Screen - Genome Cross-species aligner) to detect contamination from foreign organisms in genome sequences.
biodiversitybioinformaticsbiologyconservationgeneticgenomiclife sciences
The Genome Ark hosts genomic information for the Vertebrate Genomes Project (VGP) and other related projects. The VGP is an international collaboration that aims to generate complete and near error-free reference genomes for all extant vertebrate species. These genomes will be used to address fundamental questions in biology and disease, to identify species most genetically at risk for extinction, and to preserve genetic information of life.
bioinformaticscoronavirusCOVID-19healthlife sciencesmedicineSARS
This dataset is a collection of anonymized thoracic radiographs (X-Rays) and computed tomography (CT) scans of patients with suspected COVID-19. Images are acommpanied by a positive or negative diagnosis for SARS-CoV2 infection via RT-PCR. These images were provided by Hospital das Clínicas da Universidade de São Paulo, Hospital Sirio-Libanes, and by Laboratory Fleury.
bioinformaticsbiologygeneticgenomiclife sciences
The UCSC Genome Browser is an online graphical viewer for genomes, a genome browser, hosted by the University of California, Santa Cruz (UCSC). The interactive website offers access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. This dataset is a copy of the MySQL tables in MyISAM binary and tab-sep format and all binary files in custom formats, sometimes referred as 'gbdb'-files. Data from the UCSC Genome Browser is free and open for use by anyone. However, every genome...
agriculturebiodiversitybioinformaticsbiologyfood securitygeneticgenomiclife scienceswhole genome sequencing
This dataset captures Sunflower's genetic diversity originating from thousands of wild, cultivated, and landrace sunflower individuals distributed across North America.The data consists of raw sequences and associated botanical metadata, aligned sequences (to three different reference genomes), and sets of SNPs computed across several cohorts.
biodiversitybioinformaticsconservationearth observationlife sciences
iNaturalist is a community science effort in which participants share observations of living organisms that they encounter and document with photographic evidence, location, and date. The community works together reviewing these images to identify these observations to species. This collection represents the licensed images accompanying iNaturalist observations.
bioinformaticsgenomegenomicHomo sapienslife sciencesMus musculusnon-human primateopen source softwareRattus norvegicusvariant annotation
GenomeKit is Deep Genomics’ Python library for fast and easy access to genomic resources such as sequence, data tracks, and annotations. The goal is to let machine learning researchers build data sets easily, and to be creative about how those data sets are designed. Out of the box, GenomeKit provides access to pre-built optimized genomic data files that are required for its operation.
bioinformaticsgenomicgenotypingHomo sapienslife scienceslong read sequencingwhole genome sequencing
The Platinum Pedigree Consortium (PCC) is a collaborative project to create a comprehensive reference for human genetic variation using a four-generation, 28-member family (CEPH-1463). We employed five different short and long-read sequencing technologies to generate phased assemblies and characterize both inherited and de novo variation, including at some of the most difficult to genotype genomic regions such as tandem repeats, centromeres, and the Y chromosome. This extensive "truth set" is publicly available and can be used to test and benchmark new algorithms and technologies to ...
amazon.sciencebioinformaticsfastqgeneticgenomiclife scienceslong read sequencingshort read sequencingwhole exome sequencingwhole genome sequencing
To facilitate benchmarking and development, the Google Brain group has sequenced 9 human samples covering the Genome in a Bottle truth sets on different sequencing instruments, sequencing modalities (Illumina short read and Pacific BioSciences long read), sample preparation protocols, and for whole genome and whole exome capture. The original source of these data are gs://google-brain-genomics-public.
biodiversitybioinformaticsbiologyconservationgeneticgenomiclife sciences
Minderoo Foundation OceanOmics aims to establish environmental DNA (eDNA) as a tool to measure, understand, and protect oceans. OceanOmics mainly generates two types of data: eDNA sequencing data (metabarcoding, metagenomics), and genome assembly data (marine vertebrates).
SocialGene RefSeq Databases
amino acidbioinformaticschemical biologygenomicgraphmetagenomicsmicrobiomepharmaceuticalprotein
Precomputed SocialGene Neo4j graph databases of various sizes built from RefSeq genomes and MIBiG BGCs.
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