Tools   Select Another Resource Report Type

https://www.ncbi.nlm.nih.gov/projects/mutagene/

Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity.

Proper citation: MutaGene (RRID:SCR_016574) Copy   

•   Source: SciCrunch Registry

https://github.com/dpeerlab/phenograph

Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.

Proper citation: Phenograph (RRID:SCR_016919) Copy   

•   Source: SciCrunch Registry

https://anvilproject.org/

Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces.

Proper citation: Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) Copy   

•   Source: SciCrunch Registry

http://grantome.com/grant/NIH/U01-DK099919-04S1

Consortium to design and conduct pilot and feasibility studies of novel therapies to reduce morbidity and mortality for patients treated with maintenance hemodialysis. Data Coordinating Center (DCC) for consortium provides scientific expertise and operational support for pilot studies that will be conducted at HDPSC Participating Clinical Centers. Data Coordinating Center for Hemodialysis Pilot Studies Consortium.

Proper citation: Hemodialysis Pilot Studies Consortium (RRID:SCR_017468) Copy   

•   Source: SciCrunch Registry

https://bioinfo3d.cs.tau.ac.il/PatchDock/

Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles.

Proper citation: PatchDock (RRID:SCR_017589) Copy   

•   Source: SciCrunch Registry

http://www.immunexpresso.org

Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions.

Proper citation: immuneXpresso (RRID:SCR_017578) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/BepiPred/index.php

Sequential B-Cell Epitope Predictor. Web server predicts B-cell epitopes from protein sequence. Sequence-based B-cell epitope prediction using conformational epitopes. Sequences of protein of interest should be in fasta format. BepiPred 2.0 is available as stand alone software package, with same functionality as web service., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BepiPred-2.0 (RRID:SCR_018499) Copy   

•   Source: SciCrunch Registry

https://sedfitsedphat.nibib.nih.gov/software/default.aspx

Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.

Proper citation: SEDFIT (RRID:SCR_018365) Copy   

•   Source: SciCrunch Registry

https://usdrn.org/

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   

•   Source: SciCrunch Registry

https://www.synapse.org/#!Synapse:syn22345748/wiki/605339

Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets.

Proper citation: Exemplar Microscopy Images of Tissues (RRID:SCR_021052) Copy   

•   Source: SciCrunch Registry

https://nwb-extensions.github.io/

Community led catalog of extensions to Neurodata Without Borders data standard.

Proper citation: Neurodata Extensions Catalog (RRID:SCR_021340) Copy   

•   Source: SciCrunch Registry

https://aushsi.shinyapps.io/baseline/

Web tool to detect under- or over-dispersion in a baseline table from baseline table.

Proper citation: baseline (RRID:SCR_025128) Copy   

•   Source: SciCrunch Registry

https://www.npatlas.org

Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles.

Proper citation: Natural Products Atlas (RRID:SCR_025107) Copy   

•   Source: SciCrunch Registry

https://www.danforthcenter.org/our-work/core-facilities/advanced-bioimaging-laboratory/

Core provides instruments for live cell imaging including Leica SP8-X confocal microscope and other fluorescence microscopes. Facility provides workstation for confocal image processing, ancillary equipment required for transmission electron microscopy. Services are provided as self services after user training by IMF staff or as full services done by core facility staff.

Proper citation: Donald Danforth Plant Science Center Advanced Bioimaging Laboratory Core Facility (RRID:SCR_018951) Copy   

•   Source: SciCrunch Registry

https://www.cincinnatichildrens.org/research/support/clinical-translational-research

Clinical research support center for investigators and industry sponsors.Provides support services, research tools, experienced research personnel, and facilities to conduct or facilitate pediatric and adult clinical research from identification and development of research opportunities to phase I through phase IV clinical research trials.

Proper citation: Cincinnati Children's Hospital Office for Clinical and Translational Research Core Facility (RRID:SCR_022633) Copy   

•   Source: SciCrunch Registry

https://nationalmaglab.org/user-facilities/high-b-t-facility

Facility to conduct experiments in high magnetic fields up to 15 tesla and at very low temperatures down to 0.4 mK simultaneously. Located at University of Florida in Gainesville, it is operated as part of Physics Department Microkelvin Laboratory.

Proper citation: National High Magnetic Field Laboratory High B/T Core Facility (RRID:SCR_017360) Copy   

•   Source: SciCrunch Registry

https://sbpdiscovery.org/research/shared-resources/flow-cytometry/

Facility that provides access to high-speed cell sorting, analytical flow cytometry, imaging flow cytometry, and validated immune profiling spectral antibody panels. Core staff provide technical expertise in experiment design, data analysis, hardware and software training, operate the facility cell sorters, and are available to assist with analysis experiments for those who prefer to have their samples run by an expert cytometrist.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Flow Cytometry Core Facility (RRID:SCR_014854) Copy   

•   Source: SciCrunch Registry

https://www.unmc.edu/chvr/research/core-facilities/bioassay-core.html

Core provides equipment, personnel, and protocols for routine and advanced cellular and molecular assays for research.

Proper citation: University of Nebraska Medical Center Bioassay Core Facility (RRID:SCR_026270) Copy   

•   Source: SciCrunch Registry

https://www.ou.edu/structuralbiology/cobre-core-facilities/ppc

Offers access to instrumentation, training, and services for protein expression, purification, and biophysical characterization. In addition to instrument access, PPCC personnel offer advice, hands-on training, education, and collaboration. Provides a range of protein purification and characterization equipment.

Proper citation: University of Oklahoma Protein Production and Characterization Core Facility (RRID:SCR_028067) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/google-refine/

Software tool that stores definitions of views of data, along with the ontology concepts they represent. This is a part of the Neuroscience Information Framework (NIF) code stack.

Proper citation: ConceptMapper (RRID:SCR_006548) Copy   

•   Source: SciCrunch Registry