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https://bioconductor.org/packages/release/data/annotation/html/hgu133plus2.db.html

Software R package for Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data assembled using data from public repositories.

Proper citation: hgu133plus2 (RRID:SCR_026448) Copy   

•   Source: SciCrunch Registry
  

https://www.accordionstudy.org/public/dspHome.cfm

A prospective, observational follow-up study of at least 8000 participants who were treated and followed in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) Trial. Treatment in ACCORD ended in 2009 and ACCORDION is designed to further elucidate the long-term effects of the ACCORD treatment strategies and provide additional data on the relationships among various cardiovascular and diabetic risk factors.

Proper citation: Action to Control Cardiovascular Disease Risk in Diabetes Follow-up Study (ACCORDION) (RRID:SCR_014373) Copy   

•   Source: SciCrunch Registry
  

https://hci-bio-app.hci.utah.edu/gnomex/

A Genomic Laboratory Information Management System (LIMS) and Data repository that can function as an experiment tracking and workflow management system for Core Facilities as well as an advanced data repository for storing and sharing genomic data sets.

Proper citation: GNomEx (RRID:SCR_011805) Copy   

•   Source: SciCrunch Registry
  

https://codeocean.com/

Cloud-based executable research platform for discovering and running scientific code. Code Ocean is designed to give researchers and developers a way to share, discover and run code published in academic journals and conferences. Users can upload code and data in various programming languages and link working code in a computational environment with the associated article, with Code Ocean assigning a Digital Object Identifier (DOI) to the algorithm.

Proper citation: Code Ocean (RRID:SCR_015532) Copy   

•   Source: SciCrunch Registry
  

http://www.ncbi.nlm.nih.gov/genome/viruses/variation/

A repository which supports the search, retrieval, and display of large virus sequence data sets concerning the viruses of Dengue, West Nile, and Influenza. Users can search sequences based on a number of biological and clinical criteria and selected sequences can be downloaded or analyzed using a variety of web-based tools and displays. Virus Variation is an extension of NCBI's Influenza Virus Resource.

Proper citation: Virus Variation (RRID:SCR_013790) Copy   

•   Source: SciCrunch Registry
  

http://www.metabolomicsworkbench.org

Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops.

Proper citation: Metabolomics Workbench (RRID:SCR_013794) Copy   

•   Source: SciCrunch Registry
  

https://github.com/kpbioteam/docker_ewas

Software suite for population epigenetics integrated into Galaxy. Galaxy Docker repository for population epigenetics data analysis.

Proper citation: ewas-galaxy (RRID:SCR_018085) Copy   

•   Source: SciCrunch Registry
  

https://ncri1.partners.org/ProACT/Document/DisplayLatest/9

Publicly available repository of merged ALS clinical trials data.

Proper citation: PRO-ACT database (RRID:SCR_023520) Copy   

•   Source: SciCrunch Registry
  

http://umcd.humanconnectomeproject.org

Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately.

Proper citation: USC Multimodal Connectivity Database (RRID:SCR_012809) Copy   

•   Source: SciCrunch Registry
  

http://www.emouseatlas.org/emap/eHistology/kaufman/index.php?plate=38&image=38bb

Image repository that allows researchers to interactively explore a collection of cellular-resolution colour histology images detailing mouse development. The original histological sections have been re-digitised at high resolution, in colour and in collaboration with Elsevier, the eHistology Atlas provides the annotations as presented in the original printed version.

Proper citation: eHistology (RRID:SCR_015887) Copy   

•   Source: SciCrunch Registry
  

http://roar.eprints.org/

Listing of institutional repositories for depositing preprints of published materials with the aim of promoting the development of open access by providing timely information about the growth and status of repositories throughout the world. Open access to research maximizes research access and thereby also research impact, making research more productive and effective. Repository Types: * Research Institutional or Departmental * Research Multi-institution Repository * Research Cross-Institutional * e-Journal/Publication * e-Theses * Database/A&I Index * Research Data * Open and Linked Data * Learning and Teaching Objects * Demonstration * Web Observatory * Other Repository Software: * ARNO * Bepress * CDS Invenio * ContentDM by OCLC * DIGIBIB * DigiTool * DiVA * DoKS * DSpace * EDOC * EPrints * Equella * ETD-db * Fedora ** Fez * Greenstone * HAL * i-Tor * IntraLibrary * Keystone DLS * MiTOS * MyCoRe * Open Journal System * Open Repository * OPUS (Open Publications System) * Other softwares (various) * PMB Services * SBCAT * SciX * SobekCM * WIKINDX * Zentity

Proper citation: ROAR (RRID:SCR_005951) Copy   

•   Source: SciCrunch Registry
  

http://ccr.coriell.org/Sections/Collections/IPBIR/?SsId=18

The purpose of the IPBIR - Integrated Primate Biomaterials and Information Resource is to assemble, characterize, and distribute high-quality DNA samples of known provenance with accompanying demographic, geographic, and behavioral information in order to stimulate and facilitate research in primate genetic diversity and evolution, comparative genomics, and population genetics. Further research in these areas will advance our understanding of human origins, the biological basis of cognitive processes, evolutionary history and relationships, and social structure, and will provide critical scientific information needed to facilitate conservation of biological diversity. The derived DNA will be openly available to the broad scientific community who agree to restrict use to non-commercial purposes. DNA and cell culture samples are distributed only to qualified professional persons who are associated with recognized research, medical, or educational organizations engaged in research.

Proper citation: IPBIR - Integrated Primate Biomaterials and Information Resource (RRID:SCR_004614) Copy   

•   Source: SciCrunch Registry
  

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi

An online repository which houses sequencing data from gel and capillary platforms (such as Applied Biosystems ABI 3730®). Most sequences are derived from Whole Genome Shotgun sequencing. Large data sets as well as only a few sequences can be obtained.

Proper citation: Trace Archive (RRID:SCR_013788) Copy   

•   Source: SciCrunch Registry
  

http://humanconnectome.org/connectome/connectomeDB.html

Data management platform that houses all data generated by the Human Connectome Project - image data, clinical evaluations, behavioral data and more. ConnectomeDB stores raw image data, as well as results of analysis and processing pipelines. Using the ConnectomeDB infrastructure, research centers will be also able to manage Connectome-like projects, including data upload and entry, quality control, processing pipelines, and data distribution. ConnectomeDB is designed to be a data-mining tool, that allows users to generate and test hypotheses based on groups of subjects. Using the ConnectomeDB interface, users can easily search, browse and filter large amounts of subject data, and download necessary files for many kinds of analysis. ConnectomeDB is designed to work seamlessly with Connectome Workbench, an interactive, multidimensional visualization platform designed specifically for handling connectivity data. De-identified data within ConnectomeDB is publicly accessible. Access to additional data may be available to qualified research investigators. ConnectomeDB is being hosted on a BlueArc storage platform housed at Washington University through the year 2020. This data platform is based on XNAT, an open-source image informatics software toolkit developed by the NRG at Washington University. ConnectomeDB itself is fully open source.

Proper citation: ConnectomeDB (RRID:SCR_004830) Copy   

•   Source: SciCrunch Registry
  

https://anima.irisa.fr

Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows.

Proper citation: Anima (RRID:SCR_017017) Copy   

•   Source: SciCrunch Registry
  

http://marmosetbrain.org/

Brain connectivity atlas to create systematic, digital repository for data on connections between different cortical areas, in primate species. Data repository for connections between different cortical areas in marmoset monkeys. Allows access to data set and enables other interpretations of data, in light of future evolution of knowledge about marmoset cortex.

Proper citation: Marmoset Brain Connectivity Atlas (RRID:SCR_015964) Copy   

•   Source: SciCrunch Registry
  

https://ropensci.org

A software repository which provides and builds open source tools for open science. rOpenSci provides packages that allow access to data repositories through the R statistical programming environment. R packages are grouped by what the tools do: acquire data, full-text of journal articles, altmetrics, data-publication, reproducibility, and data visualization.

Proper citation: rOpenSci (RRID:SCR_013986) Copy   

•   Source: SciCrunch Registry
  

http://www.metabolomexchange.org/site/

International effort whose objective is to improve and encourage the exchange of Metabolomics data. Datasets are stored in external data repositories independent of MetabolomeXchange; however, MetabolomeXchange allows users to browse datasets directly then proceed to the external repository for more information.

Proper citation: MetabolomeXchange (RRID:SCR_014664) Copy   

•   Source: SciCrunch Registry
  

https://library.ucsd.edu/research-and-collections/digital-collections/dams.html

A digital repository designed to store and manage digital assets of UC San Diego. The flexible architecture can accept a variety of data formats, schemas and web services when ingesting digital assets. It stores digital content files and allows for the creation, indexing and searching of associated metadata to locate and retrieve the content files. Content can be composed of files in any format, including text, sound, video, and images. The DAMS is also designed to facilitate the transfer and submission of the Library's digital assets to Chronopolis and the California Digital Library's Merritt, and can easily be extended to serve other purposes. Additionally, the DAMS is able to export data in many formats, including METS, HTML, OAI, RSS, CSV. Future plans include linking data sets with other universities and organizations. For more information about the DAMS, including the data model and technical diagram, see Github, https://github.com/ucsdlib: * DAMS Manual, https://github.com/ucsdlib/dams/wiki/DAMS-Manual * DAMS Hydra Head, https://github.com/ucsdlib/damspas * DAMS REST API, https://github.com/ucsdlib/dams/wiki/REST-API * DAMS Ontology, https://github.com/ucsdlib/dams/tree/master/ontology Additional information on Hydra is available at Project Hydra and Duraspace.

Proper citation: Digital Asset Management System (RRID:SCR_000491) Copy   

•   Source: SciCrunch Registry
  

http://cocomac.g-node.org/main/index.php?

Online access (html or xml) to structural connectivity ("wiring") data on the Macaque brain. The database has become by far the largest of its kind, with data extracted from more than four hundred published tracing studies. The main database, contains data from tracing studies on anatomical connectivity in the macaque cerebral cortex. Also available are a variety of tools including a graphical simulation workbench, map displays and the CoCoMac-Paxinos-3D viewer. Submissions are welcome. To overcome the problem of divergent brain maps ORT (Objective Relational Transformation) was developed, an algorithmic method to convert data in a coordinate- independent way based on logical relations between areas in different brain maps. CoCoMac data is used to analyze the organization of the cerebral cortex, and to establish its structure- function relationships. This includes multi-variate statistics and computer simulation of models that take into account the real anatomy of the primate cerebral cortex. This site * Provides full, scriptable open access to the data in CoCoMac (you must adhere to the citation policy) * Powers the graphical interface to CoCoMac provided by the Scalable Brain Atlas * Sports an extensive search/browse wizard, which automatically constructs complex search queries and lets you further explore the database from the results page. * Allows you to get your hands dirty, by using the custom SQL query service. * Displays connectivity data in tabular form, through the axonal projections service. CoCoMac 2 was initiated at the Donders Institute for Brain, Cognition and Behaviour, and is currently supported by the German neuroinformatics node and the Computational and Systems Neuroscience group at the Juelich research institute.

Proper citation: CoCoMac (RRID:SCR_007277) Copy   

•   Source: SciCrunch Registry