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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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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WASP Resource Report Resource Website 1+ mentions |
WASP (RRID:SCR_025497) | software resource, software toolkit, source code | Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery. | molecular QTLs discovery, unbiased allele-specific read mapping and discovery, molecular QTLs, unbiased allele-specific read, mapping and discovery, | Howard Hughes Medical Institute ; NHGRI HG006123; NHGRI HG007036; NIGMS GM007197; NIMH MH101825; NSF |
PMID:26366987 | Free, Available for download, Freely available, | SCR_025497 | 2026-09-19 01:00:26 | 3 | |||||||||
|
PaleoClim database Resource Report Resource Website 10+ mentions |
PaleoClim database (RRID:SCR_025657) | data or information resource, database | Database of downscaled paleoclimate outputs at 2.5 minute resolution (~5 km at equator) that includes surface temperature and precipitation estimates from snapshot-style climate model simulations using HadCM3, a version of the UK Met Office Hadley Centre General Circulation Model. Database contains climatic data for three key time periods spanning from 3.3 to 0.787 million years ago: the Marine Isotope Stage 19 (MIS19) in the Pleistocene (~787 ka), the mid-Pliocene Warm Period (~3.264–3.025 Ma), and MIS M2 in the Late Pliocene (~3.3 Ma). Set of historical climate layers (climate grids) with spatial resolution of about 2.5 min. These data can be used for mapping and spatial modelling in Geographic Information Systems (GIS) or other computer programs. | historical climate layers, climate grids, paleoclimate outputs, 2.5 minute resolution, surface temperature, precipitation estimates, climate model simulations, climatic data, | European Research Council ; National Aeronautics and Space Administration ; NSF ; São Paulo State Research Foundation ; Southern Illinois University ; University of Leeds International Research Collaboration Award |
PMID:30422125 | Free, Freely available | SCR_025657 | Paleoclim | 2026-09-19 01:00:31 | 28 | ||||||||
|
tTFtarget Resource Report Resource Website 1+ mentions |
tTFtarget (RRID:SCR_025631) | data or information resource, database | Transcription factor target database. Platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments and target genes or transcripts across multiple organisms. | Transcription factor target, validated binding sites, transfer RNA-derived fragments, target genes, multiple organisms, | NLM R01LM014087; NSF |
DOI:10.1093/nar/gkad815 | Free, Freely available | SCR_025631 | tRFtarget 2.0, tRFtarget 1.0 | 2026-09-19 01:00:30 | 4 | ||||||||
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SIMS Resource Report Resource Website 1+ mentions |
SIMS (RRID:SCR_025787) | software application, software resource | Software label transfer tool for single-cell RNA sequencing analysis. Scalable, Interpretable Modeling for Single-cell RNA-seq data classification. | label transfer, single-cell RNA sequencing analysis, single-cell RNA-seq data classification, | NHGRI 1RM1HG011543; NIMH 1U24MH132628; NSF ; QualcommInstitute ; Schmidt Futures ; University of California Office of the President |
PMID:38823397 | Free, Available for download, Freely available | SCR_025787 | scalable, interpretable machine learning for single cell | 2026-09-19 01:00:35 | 2 | ||||||||
|
Predictomes Resource Report Resource Website 1+ mentions |
Predictomes (RRID:SCR_026691) | data or information resource, database | Interactive database of protein protein interactions modeled by AlphaFold multimer. Classifier-curated database of AlphaFold-modeled protein-protein interactions. | Classifier-curated database, AlphaFold-modeled protein-protein interactions, interactive database, protein protein interactions, | NHLBI HL098316; NSF |
PMID:38645019 | Free, Freely available | SCR_026691 | 2026-09-19 01:00:55 | 5 | |||||||||
|
RFMix Resource Report Resource Website 1+ mentions |
RFMix (RRID:SCR_027030) | software application, software resource | Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference. | Discriminative Modeling, local ancestry and admixture inference, | NHGRI 2R01HG003229; NLM LM007033; NSF |
PMID:23910464 | Restricted | SCR_027030 | 2026-09-19 01:01:03 | 9 | |||||||||
|
RagTag Resource Report Resource Website 50+ mentions |
RagTag (RRID:SCR_027293) | software resource, software toolkit, source code | Collection of software tools for scaffolding and improving modern genome assemblies. Reference-based scaffolder. Used for fast and flexible genome assembly scaffolding and improvement. | Reference-based scaffolder, genome assembly scaffolding, scaffolding, genome assemblies, | European Research Council ; Howard Hughes Medical Institutes ; NIH Office of the Director S10OD028632; NSF ; Swiss National Science Foundation |
PMID:36522651 | SCR_027293 | 2026-09-19 01:01:08 | 91 | ||||||||||
|
OpenMEE Resource Report Resource Website 1+ mentions |
OpenMEE (RRID:SCR_027300) | data analysis software, data processing software, software application, software resource | Open-source, cross-platform software for ecological and evolutionary meta-analysis. | ecological and evolutionary meta-analysis, ecological, evolutionary, meta-analysis, | NSF | DOI:10.1111/2041-210X.12708 | Free, Available for download, Freely available | SCR_027300 | 2026-09-19 01:01:08 | 6 | |||||||||
|
PyReconstruct Resource Report Resource Website 1+ mentions |
PyReconstruct (RRID:SCR_027562) | software application, software resource, source code | Software successor to the Reconstruct annotation tool. PyReconstruct runs on all major operating systems, breaks through legacy RAM limitations, features intuitive and collaborative curation system, and employs flexible and dynamic approach to image registration. Used to analyze, display, and publish experimental or connectomics data. Suited for generating ground truth to implement in automated segmentation, outcomes of which can be returned to PyReconstruct for proofreading and quality control. | analyze, display, publish, experimental data, connectomics data, | NIMH R56MH139176; NSF |
PMID:40737319 | Free, Available for download, Freely available | SCR_027562 | 2026-09-19 01:01:13 | 2 | |||||||||
|
PySeq2500 Resource Report Resource Website |
PySeq2500 (RRID:SCR_027678) | software application, software resource, source code | Software tool to control Illumina HiSeq 2500 System. Open source Python code base and flow cell design that converts Illumina HiSeq 2500 instrument, comprising epifluorescence microscope with integrated fluidics, into open platform for programmable applications without need for specialized engineering or software development expertise.Enables non-specialists to develop and implement fluidics coupled imaging methods in benchtop system. | control Illumina HiSeq 2500 System, develop and implement fluidics coupled imaging, | works with: Illumina: HiSeq 2500 System | NSF | DOI:10.1038/s41598-022-08740-w | Free, Available for download, Freely available | https://regenseq.github.io/ | SCR_027678 | 2026-09-19 01:01:15 | 0 | |||||||
|
Diffusion-Model Resource Report Resource Website 1+ mentions |
Diffusion-Model (RRID:SCR_027942) | software resource, source code | Software code for simulating diffusion in brain extracellular space images. | simulating diffusion, brain, extracellular space, images | NINDS R01NS130759; NSF ; Spanish Government |
PMID:41279667 | Free, Available for download, Freely available | SCR_027942 | , Diffusion Flux, DifFlux, Diffusion Flux Model | 2026-09-19 01:01:21 | 1 | ||||||||
|
University of Oklahoma Biomolecular Structure Core Facility Resource Report Resource Website 1+ mentions |
University of Oklahoma Biomolecular Structure Core Facility (RRID:SCR_028074) | access service resource, core facility, service resource | Offers access to instrumentation, training and services for structure determination of macromolecular molecules using single crystal X-ray diffraction and/or cryo-EM Single Particle Analysis (SPA). Instrumentation is available for initial crystallization trials, optimization of crystallization, single crystal X-ray diffraction and data collection at synchrotron radiation facilities, as well as electron microscopy grid preparation for cryo-EM (SPA), screening and data collection using a Thermo Scientific Tundra Cryo-TEM and assistance for data collection at national laboratories. | ABRF, structure determination, macromolecular molecules, single crystal, X-ray diffraction, cryo-EM Single Particle Analysis, |
is listed by: ABRF CoreMarketplace has parent organization: University of Oklahoma; Oklahoma; USA |
NIGMS P20GM103640; NIGMS P30GM145423; NSF 0922269 |
ABRF_5821 | https://coremarketplace.org/RRID:SCR_028074/?citation=1 | SCR_028074 | 2026-09-19 01:01:24 | 1 | ||||||||
|
CellTool Resource Report Resource Website 10+ mentions |
CellTool (RRID:SCR_028232) | software application, software resource, standalone software | Stand-alone open-source software with graphical user interface for analysis of time-lapse microscopy images. Combines bio-image analysis and mathematical modeling for study of DNA repair dynamics. | analysis of time-lapse microscopy images, time-lapse microscopy images, | NSF | PMID:38069107 | Free, Available for download, Freely available | SCR_028232 | 2026-09-19 01:01:27 | 14 | |||||||||
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Bruker: Avance Neo 1.2 GHz NMR Spectrometer Resource Report Resource Website |
Bruker: Avance Neo 1.2 GHz NMR Spectrometer (RRID:SCR_028512) | instrument resource | Spectrometer represents the pinnacle of commercial nuclear magnetic resonance technology. Operating at 28.2 Tesla, this ultra-high-field system is primarily used for advanced structural biology, pharmaceutical research, and materials science. Delivers the highest commercially available spectral resolution, crucial for investigating complex protein dynamics, functional molecular disorders, and viral structures. Console:Avance Neo; Magnet:Gateway; Field Strength: 1.2 GHz; Software:TopSpin 4.4.1 on CentOS 7; Probes:3mm TCI cryoprobe; 3mm BBI room-temperature; 3.2mm HX low-gamma MAS; 1.9mm HX high-gamma MAS; 1.3mm HCN fast MAS; 0.7mm HCN ultra-fast MAS; Chilled SampleCase (up to 24 samples); Automated Tuning and Matching (ATM); Nitrogen Liquefier. | NMR, spectrometer, Gateway 1.2 GHz NMR, | is used by: Ohio State University Campus Chemical Instrument Center NMR Core Facility | NSF RI-1 1935913 | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028512.pdf | Model_Number_Bruker_Avance_Neo_Gateway_1.2 GHz | https://people.ohioinnovationexchange.org/equipment/1696125, https://www.bruker.com/en/products-and-solutions/mr/nmr/avance-nmr-spectrometer.html | SCR_028512 | , Avance Neo 1.2 GHz NMR Spectrometer system, Bruker: Avance Neo Gateway 1.2 GHz NMR Spectrometer system | 2026-09-19 01:01:33 | 0 | |||||
|
CytoVerse Resource Report Resource Website |
CytoVerse (RRID:SCR_028854) | data access protocol, data analysis software, data processing software, data visualization software, software application, software resource, web service | Web application to map single-cell RNA data into AI foundation model spaces. Lets search millions of reference cells and view cell types locally without uploading private data or needing powerful cloud servers. Using ONNX model deployment and compressed IVFPQ indexing, it annotates local datasets against a 23-million-cell reference without server computation, installation, or data upload, and shares embeddings as lightweight files, enabling private, interactive, and collaborative single-cell analysis. | single-cell RNA-seq, foundation models, browser based analysis, WebAssembly, ONNX, scFM, approximate nearest neighbors, latent space collaboration, data privacy, | Brain and Behavior Research Foundation ; California Institute for Regenerative Medicine ; NHGRI RM1HG011543; NIMH U24MH132628; NINDS U24NS146314; NSF ; University of California Office of the President |
PMID:41659670 | Free, Available for download, Freely available | https://github.com/braingeneers/cytoverse | SCR_028854 | 2026-09-19 01:01:41 | 0 | ||||||||
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ComBat-seq Resource Report Resource Website |
ComBat-seq (RRID:SCR_028999) | software application, software resource, source code | Software batch effect adjustment tool for bulk RNA-seq count data. | batch correction, batch effect adjustment, bulk RNA-seq count data, | NCI 4P30CA006516; NCI 5U01 CA220413; NIGMS 5R01GM127430; NSF |
PMID:33015620 | Free, Available for download, Freely available | SCR_028999 | 2026-09-19 01:01:45 | 0 |
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