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https://dataverse.org/

Project portal for publishing, citing, sharing and discovering research data. Software, protocols, and community connections for creating research data repositories that automate professional archival practices, guarantee long term preservation, and enable researchers to share, retain control of, and receive web visibility and formal academic citations for their data contributions. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive appropriate credit. Hosts multiple dataverses. Each dataverse contains studies or collections of studies, and each study contains cataloging information that describes the data plus the actual data files and complementary files. Data related to social sciences, health, medicine, humanities or other sciences with an emphasis in human behavior are uploaded to the IQSS Dataverse Network (Harvard). You can create your own dataverse for free and start adding studies for your data files and complementary material (documents, software, etc). You may install your own Dataverse Network for your University or organization.

Proper citation: Dataverse Network Project (RRID:SCR_001997) Copy   

•   Source: SciCrunch Registry

http://amigo.geneontology.org/

Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium.

Proper citation: AmiGO (RRID:SCR_002143) Copy   

•   Source: SciCrunch Registry

http://htslib.org/

Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.

Proper citation: SAMTOOLS (RRID:SCR_002105) Copy   

•   Source: SciCrunch Registry

http://openneuro.org

Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data.

Proper citation: OpenNeuro (RRID:SCR_005031) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://genome.ucsc.edu/

Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.

Proper citation: UCSC Genome Browser (RRID:SCR_005780) Copy   

•   Source: SciCrunch Registry

http://mialab.mrn.org/index.html

MIALAB, headed by Dr. Vince Calhoun, focuses on developing and optimizing methods and software for quantitative analysis of structure and function in medical images with particular focus on the study of psychiatric illness. We work with many types of data, including functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI), electroencephalography (EEG), structural imaging and genetic data. Much of our time is spent working on new methods for flexible analysis of brain imaging data. The use of data driven approaches is very useful for extracting potentially unpredictable patterns within these data. However such methods can be further improved by incorporating additional prior information as constraints, in order to benefit from what we know. To this end, we draw heavily from the areas of image processing, adaptive signal processing, estimation theory, neural networks, statistical signal processing, and pattern recognition.

Proper citation: MIALAB - Medical Image Analysis Lab (RRID:SCR_006089) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

Proper citation: Bioconductor (RRID:SCR_006442) Copy   

•   Source: SciCrunch Registry

http://dsarm.niapublications.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 18, 2014.

A networking site for investigators using animal models to study aging, developed to provide a venue for sharing information about research models for aging studies. If you have tissue or data from animal models relevant to aging research that you are willing to share with other investigators, D-SARM allows you to identify the model and provides a secure, blinded email contact for investigators who would like to contact you about acquiring tissue or related resources. Investigators looking for resources from a particular model enter search terms describing the model of interest and then use the provided link to send emails to the contacts (names blinded) listed in the search results to initiate dialog about tissue or resources available for sharing. The database is housed on a secure server and admission to the network is moderated by the NIA Project Officer and limited to investigators at academic, government and non-profit research institutions. The goal is to provide a secure environment for sharing information about models used in aging research, promoting the sharing of resources, facilitating new research on aging in model systems, and increasing the return on the investment in research models.

Proper citation: Database for Sharing Aging Research Models (RRID:SCR_008691) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/

Repository of open source tools for behavioral neuroscience research. OpenBehavior features hardware (tools, devices, apparatuses), as well as software for data acquisition and analysis and for the investigation of animal behavior and cognition. Dedicated to accelerating research through promotion of collaboration and open source projects.

Proper citation: OpenBehavior (RRID:SCR_015938) Copy   

•   Source: SciCrunch Registry

http://montana.eagle-i.net/i/0000012b-00be-4e65-df3b-3fdc80000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research.

Proper citation: Montana State University Bioinformatics Core Facility (RRID:SCR_009937) Copy   

•   Source: SciCrunch Registry

https://wistar.org/research-discoveries/shared-resources/bioinformatics-facility

Core provides High Throughput Data Analysis, Customized Bioinformatics Services, Custom Programming, High Performance Computing, Data management. Located in the Center for Systems and Computational Biology. Provides Cancer Center investigators with database management, software application support, expertise in statistical analyses and computational modeling of biomedical research data.

Proper citation: Wistar Bioinformatics Core Facility (RRID:SCR_010203) Copy   

•   Source: SciCrunch Registry

http://www.cbrc.jp/htbin/show_tffactor_mw

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 13, 2016.

A dataset about transcriptional regulation in eukaryotic cells, including data such as transcription factors and their binding sites and profiles. Resource is in Chinese.

Proper citation: TFFACTOR (RRID:SCR_000519) Copy   

•   Source: SciCrunch Registry

http://www.rand.org/labor/FLS/MHSS.html

A data set of the health and socioeconomic factors that affect the elderly in Matlab, a region of rural Bangladesh. The survey captures measurements and statistics such as adult survival, health status, health care utilization, resource flows between generations and the impact of community services and infrastructure on adult health care. Data was collected through surveys that touch on four topics: household and individual information; determinants of natural fertility; migration out of the community; and community and provider survey of healthcare and education infrastructure.

Proper citation: Matlab Health and Socio-Economic Survey (RRID:SCR_008942) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012a-2518-fb6c-5617-794280000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics.

Proper citation: Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center (RRID:SCR_009668) Copy   

•   Source: SciCrunch Registry

https://knightadrc.wustl.edu/professionals-clinicians/request-center-resources/

Provides on request resources including Data: clinical and cognitive measures as well as MRI and amyloid imaging scans; Tissue: frozen brain tissue, paraffin brain sections, antemortem CSF, DNA, fibroblast, dermal fibroblasts, plasma (fasting and non-fasting) and iPSC; Participants: eligible participants may be invited to enroll in research of other investigators after appropriate review. Researchers can use the request portal to review Center guidelines and policies; view available data and tissue; access data tables and codebooks; and submit request for resources.

Proper citation: Washington University School of Medicine Knight ADRC Request Center Resources Core Facility (RRID:SCR_025254) Copy   

•   Source: SciCrunch Registry

https://core.bioinformatics.udel.edu

CBCB Bioinformatics Data Science Core builds upon infrastructure of the Center for Bioinformatics and Computational Biology. Delaware Biotechnology Institute , Delaware Data Science Institute, and Protein Information Resource. Core helps with planning your research or analyzing your current data. Services:Consultation and Collaboration, Proposal Assistance,Training, Bioinformatics Software, Computational Hardware, Database and Web Services, Next Gen Analysis, Custom Analysis.

Proper citation: University of Delaware CBCB Bioinformatics Data Science Core Facility (RRID:SCR_017696) Copy   

•   Source: SciCrunch Registry

https://www.albany.edu/repr/

Resource offers range of mass spectrometry instrumentation, expertise in analysis of RNA, RNA modifications, and proteins involved in RNA metabolism/regulation, supports projects involving analysis of biomolecules, metabolites, and small synthetic molecules, provides consulting on experimental design, sample preparation and data interpretation, whole project development and grant writing contributions.

Proper citation: Albany University RNA Epitranscriptomics and Proteomics Resource Core Facility (RRID:SCR_017695) Copy   

•   Source: SciCrunch Registry

https://crc.ibest.uidaho.edu/

Provides evolutionary and computational biology investigators with computing and large data storage capacity for use in analyzing and managing large volumes of research data. Core contains advanced mix of high performance computing clusters, servers and data storage components, knowledge and technical skills required to compress years of analysis into days.

Proper citation: Idaho University IBEST Computational Resources Core Facility (RRID:SCR_017734) Copy   

•   Source: SciCrunch Registry

https://sdrc.stanford.edu/sdrc-research-cores/dctc/home/

With the following services from the Diabetes Clinical and Translational Core (DCTC), members will receive training in biospecimen preservation, study design, data analysis, data management, use of statistical software and clinical trial conduct.

Proper citation: Stanford Diabetes Research Center Diabetes Clinical and Translational Core (RRID:SCR_016212) Copy   

•   Source: SciCrunch Registry

https://sdrc.stanford.edu/sdrc-research-cores/dimc/home/

Core facility that provides immune monitoring assays at the RNA, protein, and cellular level, as well as archiving, reporting, and data mining support for clinical and translational studies related to Diabetes. The DIMC is a specialized subcore of the Human Immune Monitoring Center (HIMC) at Stanford.

Proper citation: Stanford Diabetes Research Center Diabetes Immune Monitoring Core (RRID:SCR_016210) Copy   

•   Source: SciCrunch Registry