Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Platform for individuals who want to make their own data available for research. Used by people to join network with others who wish to contribute to vital research in partnership with and alongside leading scientists. Personal tool for saving and displaying medical information.
Proper citation: Hugo Data (RRID:SCR_022763) Copy
https://github.com/linnarsson-lab/loom-viewer
Software tool for sharing, browsing and visualizing single-cell data stored in the Loom file format.
Proper citation: loom-viewer (RRID:SCR_016683) Copy
Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP.
Proper citation: Human Tumor Atlas Network (RRID:SCR_023364) Copy
Integrated healthcare biobank that operates under certified conditions and strict SOPs. Enables biomedical and translational researchers to perform their analyses using high quality biospecimens and data to generate reliable and reproducible research data. Core offers modular biobanking portfolio that can cover workflow from blood collection to storage, including all pre-analytical steps and their documentation. Offers spectrum of additional services ranging from DNA/RNA extraction and virtual microscopy to entire management of sample and data flow for national and international research consortia. Provides secure conventional and automated storage of samples at various temperatures as well as secure data management.
Proper citation: Charite University and Berlin Institute for Health Research Central Biobank Core Facility (RRID:SCR_023495) Copy
Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data.
Proper citation: RedVis (RRID:SCR_024550) Copy
https://sourceforge.net/p/iris-scanning/calliope
Software package for image processing for MATLAB. Used for processing of calcium imaging data.
Proper citation: Calliope calcium imaging processing package (RRID:SCR_021213) Copy
https://cumulus.readthedocs.io/en/stable
Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.
Proper citation: Cumulus (RRID:SCR_021644) Copy
http://www.cytobank.org/index.html
A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow.
Proper citation: Cytobank (RRID:SCR_014043) Copy
Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database.
Proper citation: ChEMBL (RRID:SCR_014042) Copy
http://scanimage.vidriotechnologies.com/
Open source software application for laser scanning microscopy, electrophysiology, laser scanning photostimulation, and other physiological methods focused on neurobiology. Used to control laser scanning microscopes without need for custom data acquisition hardware. Standard data acquisition boards are used to acquire data and control laser scanning. The tasks of signal integration and image processing are placed on the computer CPU. Multiple versions of ScanImage are available, each with their own features.
Proper citation: ScanImage (RRID:SCR_014307) Copy
http://www.imb.sinica.edu.tw/core/publicfacilities/pdf/LAS-1000plus_om_e_ver2.pdf
A software which is used to control the LAS-1000plus luminescent image analyzer. This software adjusts the focus, exposure time, sensitivity, and cooling temperature, and will record the data after the sample is scanned.
Proper citation: Image Reader LAS-1000 (RRID:SCR_014585) Copy
https://github.com/najasplus/hetindel_shinyapp
Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels.
Proper citation: Hetindel (RRID:SCR_018922) Copy
Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies.
Proper citation: Urinary Stone Disease Research Network (RRID:SCR_019059) Copy
https://www.openicpsr.org/openicpsr/covid19
Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings.
Proper citation: COVID-19 Data Repository (RRID:SCR_019105) Copy
https://trials.bgcarlisle.com/
Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set.
Proper citation: Clinical Trials Viewer (RRID:SCR_019230) Copy
https://www.embrys.jp/embrys/html/About.html
Data collection of gene expression patterns mapped in whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which most striking dynamics in pattern formation and organogenesis is observed. Collection of gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. Genes were extracted from databases including RIKEN Transcription Factor Database and Panther Classification System.
Proper citation: EMBRYS (RRID:SCR_006689) Copy
Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated.
Proper citation: Open Access Series of Imaging Studies (RRID:SCR_007385) Copy
http://mousespinal.brain-map.org/about.html
Platform for exploring spinal cord at cellular and molecular levels. Map of gene expression for adult and juvenile mouse spinal cord. Provides map of normal mouse when used to compare gene expression in diseased or injury models. Interactive database of gene expression mapped across all anatomic segments of mouse spinal cord at postnatal days 4 and 56. Indexed set of images based on RNA in situ hybridization data, searchable and sortable by gene, age, expression, cervical, thoracic, lumbar, sacral, and coccygeal segments.
Proper citation: Allen Mouse Spinal Cord Atlas (RRID:SCR_007418) Copy
Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data.
Proper citation: Topology Data Bank of Transmembrane Proteins (RRID:SCR_007964) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within NIF that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
