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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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HingeProt Resource Report Resource Website 1+ mentions |
HingeProt (RRID:SCR_018136) | data access protocol, service resource, software resource, web service | Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures. | Predicting protein hinges, flexible hinge region, native topology, rigid protein part, elastic network model, protein structure, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17847101 | Free, Available for download, Freely available | biotools:hingeprot | https://bio.tools/hingeprot | SCR_018136 | SciCrunch Registry | 2026-11-07 11:58:56 | 4 | |||||||
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Beckman Coulter: Biomek i7 Hybrid Automated Workstation Resource Report Resource Website 1+ mentions |
Beckman Coulter: Biomek i7 Hybrid Automated Workstation (RRID:SCR_018094) | instrument resource | Liquid handling instrument designed to optimize dependability and walk-away time. Biomek i7 Hybrid with enclosure has up to 45 deck positions and includes both Multichannel and Span-8 pipette heads in enclosed work space. | Liquid handling, instrument, equipment, Beckman Coulter | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018094.pdf | https://bec-techdocs-prod.s3.us-west-2.amazonaws.com/techdoc/files/ifu/en/C16028AB.pdf?AWSAccessKeyId=ASIA2KJI7HMZ33DV6WQG&Expires=1701735968&Signature=2MDYEbJhW4PJy4sgXzeeS9DyO%2B8%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEP%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJGMEQCIHg6cmtDSAztedNNXtxyHC%2FQ9o4yM1SgSuLP9xeBShEqAiBzvdXKsSIHPDhKAAp89Ph3a%2F5N4WI6Q%2B2vzPWAUmArISr6AghoEAQaDDcwOTI5MjQwNzYwMyIMCupsWUjiXR86CzK6KtcCan1TNZecdLIPuEOW2TsrPrXuHumQlBikN6ce3yhHyhkat%2BXxcoT72Pefl%2FuXb8zIanpeQ2sRYiTG8XuuwjK%2B016PUCUcgWG%2FUbf4t2y12I2SLOd3YI%2FgEHK7sPoIpH2K4tkz%2FVPXgRQ8zMgYMsMSq2XxD%2F2iGkromeIhZvz1a12ertzuOrynkyfT%2FZFAWt0p2NADzT%2F8kc3WLrWByJbzv6vmPs4%2ByZPUdva6vQ6dM2F0%2F9L%2BRULmL8RsHpbOfslrhsEZY9BK%2FuoSx49fTTyKmKPs8g%2FDthw5g6r7YhAzTWk0cVagwcSRZ%2F7xdsjhGusWmQNJvFfNyz72rvaddAINSSLWsjArEdL2NUZahdlFZ%2BzbyqAC3thGwmySgtkHdEVSWmqPHvZ9o80lR9seE1mXvIVtc%2FLW2LVl76gjIxRcND2QtTZKw5CpR%2F8YtYDKySe4eBxtZux8HTD8rbmrBjqfAfP6m3jf8H5DybTLXkGz6gxd3X4fRRuizXOxQGkUA3whw298yFHAZWDEBP3LUp0cL6rJFdjvd7oEJ44qaZRNwKUtjYjk9%2FviPVWPPsZCX%2BIvmEE%2FN77lL6Dav6ASE8fjWuS3V8hnTTbo%2Filx%2F18BNJZIJ1ftJuUMhizI75F9CvvnLtweybGFoajnIOBQkN1ArufaYn%2BGCQPsVh1TOR%2F8Fw%3D%3D | SCR_018094 | SciCrunch Registry | 2026-11-07 11:58:55 | 7 | |||||||||
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seaborn Resource Report Resource Website 100+ mentions |
seaborn (RRID:SCR_018132) | data processing software, data visualization software, software application, software library, software resource, software toolkit | Software Python tool as data visualization library based on matplotlib. Provides interface for drawing attractive and informative statistical graphics. Statistical data visualization using matplotlib. | Data visualization library, statistical graphic, statistical data visualization | uses: Matplotlib | Free, Available for download, Freely available | https://github.com/mwaskom/seaborn/tree/v0.10.0 | SCR_018132 | SciCrunch Registry | 2026-11-07 11:58:55 | 479 | |||||||||
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Anatomography Resource Report Resource Website 1+ mentions |
Anatomography (RRID:SCR_018147) | service resource, software resource, web application | Web application that enables users to build and publish own custom manikins. Used to build three dimensional model of human body using parts registered in BodyParts3D. Server returns image of assembled 3D model as still image, rotating animation, interactive image, etc. Each part can be downloaded as polygon mesh file that can be used with 3D printer. | Custom manikins, 3D, body parts, three dimensional model, human body, image, rotating animation, interactive image, BodyParts3D, 3D printer | Free, Freely available | SCR_018147 | SciCrunch Registry | BodyParts3D / Anatomography | 2026-11-07 11:58:56 | 6 | ||||||||||
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ChromHMM Resource Report Resource Website 50+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, data processing software, software application, software resource | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
Alfred P. Sloan Fellowship ; CAREER Award ; NHGRI RC1HG005334; NHGRI U01 HG007912; NHGRI U54 HG004570; NIEHS R01 ES024995; NIMH U01 MH105578; NSF 0905968 |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | SciCrunch Registry | 2026-11-07 11:58:43 | 50 | ||||||
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Warp Resource Report Resource Website 10+ mentions |
Warp (RRID:SCR_018071) | data acquisition software, data analysis software, data processing software, software application, software resource | Software tool that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Corrects micrographs for global and local motion, estimates local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. Software includes deep-learning-based models for accurate particle picking and image denoising. | Automating preprocessing step, cryo EM data acquisition, micrograph correction, particle picking, image denoising, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1038/s41592-019-0580-y | Free, Available for download, Freely available | BioTools:Warp, biotools:Warp | https://bio.tools/Warp, https://bio.tools/Warp, https://bio.tools/Warp | SCR_018071 | SciCrunch Registry | 2026-11-07 11:58:55 | 10 | |||||||
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gProfiler2 Resource Report Resource Website 50+ mentions |
gProfiler2 (RRID:SCR_018190) | data analysis software, data processing software, software application, software resource | Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool. | Gene list, functional enrichment analysis, namespace conversion, data, analysis |
is listed by: ELIXIR Tools and Data Services Registry is related to: R Project for Statistical Computing works with: g:Profiler |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:31066453 | Free, Available for download, Freely available | SCR_018190 | SciCrunch Registry | gprofiler2 | 2026-11-07 11:58:56 | 63 | |||||||
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Agisoft Metashape Resource Report Resource Website 100+ mentions |
Agisoft Metashape (RRID:SCR_018119) | data processing software, image processing software, software application, software resource, standalone software | Stand alone software that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales. Successor of PhotoScan and is advanced image-based 3D modeling solution aimed at creating professional quality 3D content from still images. | Agisoft LLC, photogrammetry processing, digital image, 3D spatial data, GIS, visual effect production, 3D computer graphic |
is related to: Agisoft Photoscan is related to: Agisoft Photoscan |
SCR_018119 | SciCrunch Registry | 2026-11-07 11:58:55 | 172 | |||||||||||
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RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | data access protocol, simulation software, software application, software resource, web service | Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model. | Protein structure predictor, 3D structure, protein sequence, secondary and tertiary structure, binding site, solvent accessibility, disordered region, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
NIGMS R01 GM089753; NSF DBI 0960390 |
PMID:21987485 | Restricted | biotools:raptorx | https://bio.tools/raptorx | SCR_018118 | SciCrunch Registry | 2026-11-07 11:58:42 | 198 | ||||||
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QIIME 2 View Resource Report Resource Website 100+ mentions |
QIIME 2 View (RRID:SCR_018074) | data acquisition software, data processing software, data visualization software, service resource, software application, software resource | Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided. | QIIME 2, visualization, data, interface, file viewing, file download and displaying | Free, Freely available | https://github.com/qiime2/q2view | SCR_018074 | SciCrunch Registry | q2view | 2026-11-07 11:58:54 | 102 | |||||||||
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FlowPy Resource Report Resource Website 1+ mentions |
FlowPy (RRID:SCR_018195) | data analysis software, data processing software, data visualization software, software application, software resource | Software Python tool for flow cytometry data. Data generated by flow cytometer can be read by FlowPy. Used for data extraction, data visualization, data clustering, histogram subtraction. | Flow cytometry data, data extraction, data visualization, data clustering, histogram subtraction | Free, Available for download, Freely available | SCR_018195 | SciCrunch Registry | 2026-11-07 11:58:58 | 2 | |||||||||||
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PremierBiosoft Proteo IQ Software Resource Report Resource Website 10+ mentions |
PremierBiosoft Proteo IQ Software (RRID:SCR_018072) | data analysis software, data analytics software, data processing software, software application, software resource | Software package as comprehensive qualitative and quantitative suite for proteomics. Used to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. Provides customizable interface to support any form of biological annotation. Used to compare protein quantitative results in relation to biological pathways, protein localization, protein function, or to transcript abundance. Every protein identification can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or in-house LIMS. | Proteomic, qualitative, quantitative, protein identification, data, PREMIER Biosoft, mass spectrometry data, database search engine |
works with: GenBank works with: UniProtKB works with: IPI |
Restricted | SCR_018072 | SciCrunch Registry | ProteoIQ | 2026-11-07 11:58:55 | 35 | |||||||||
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CircaDB Resource Report Resource Website 10+ mentions |
CircaDB (RRID:SCR_018078) | CircaDB | data access protocol, data or information resource, database, software resource, web service | Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans. | Mammalian circadian gene, gene expression, expression profile, mice, human, gene annotation, data, time course expression data | PMID:23180795 | Free, Freely available | http://github.com/itmat/circadb | SCR_018078 | SciCrunch Registry | Circadian gene expression profiles DataBase | 2026-11-07 11:58:42 | 27 | |||||||
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VitalRecorder2 Resource Report Resource Website 1+ mentions |
VitalRecorder2 (RRID:SCR_018199) | data acquisition software, data processing software, software application, software resource | Sleep recording software by Kissei Comtech Co., Ltd. Can measure signals of up to 32 channels while monitoring wave forms in real time. Addition of video recording option enables simultaneous recording of biological signals and video. | Sleep recording, Kissei Comtech Co., Ltd., wave signal measure, wave form monitoring, biological signals recording | Restricted | SCR_018199 | SciCrunch Registry | 2026-11-07 11:58:44 | 4 | |||||||||||
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QuB Resource Report Resource Website 1+ mentions |
QuB (RRID:SCR_018076) | QuB | data analysis software, data processing software, software application, software resource, software toolkit | Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Ion channel biophysics, neurophysiology data, hiddent state, memoryless system, solving kinetic model, data, Markov kinetics, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018076 | SciCrunch Registry | Quantify unknown Biophysics | 2026-11-07 11:58:56 | 2 | |||||||||
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SMART-Farm Tool Resource Report Resource Website 1+ mentions |
SMART-Farm Tool (RRID:SCR_018197) | SMART, SMART-Farm | analysis service resource, data or information resource, database, production service resource, service resource, software resource, training service resource, web application | Web and offline tool for holistic sustainability assessment of farms. Tool operationalizes Sustainability Assessment of Food and Agriculture Systems Guidelines of Food and Agriculture Organisation of United Nations. Tool consists of questionnaire software, centralized database, pool of indicators and scientifically based assessment methodology. Different stakeholders can use results of this assessment e.g. for comparing different farms, production systems or for strategic development, improvement, monitoring and communication to business partners. | Sustainability assessment, food company, organic agriculture, strategic development, monitoring, Sustainable Food Systems GmbH | https://www.sustainable-food-systems.com/smart-methode/, https://www.fibl.org/en/themes/projectdatabase.html | SCR_018197 | SciCrunch Registry | Sustainability Monitoring and Assessment RouTine, smart, SMART tool, smart farm, SMART-Farm tool | 2026-11-07 11:58:57 | 1 | |||||||||
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cowplot Resource Report Resource Website 50+ mentions |
cowplot (RRID:SCR_018081) | data processing software, data visualization software, software application, software resource | Software R package as streamlined plot theme and plot annotations for ggplot2. Provides various features that help with creating publication quality figures with ggplot2, such as set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. | Plot, annotation, publication figure, image |
is listed by: CRAN works with: ggplot2 |
Free, Available for download, Freely available | https://wilkelab.org/cowplot/ | SCR_018081 | SciCrunch Registry | R package cowplot | 2026-11-07 11:58:55 | 64 | ||||||||
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Vivli Resource Report Resource Website 1000+ mentions |
Vivli (RRID:SCR_018080) | data or information resource, nonprofit organization, service resource | Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials. | Global data sharing, clinical research data, data, sharing, analytical platform, clinical trial, COVID-19-related trials |
is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is listed by: Data and Computational Resources to Address COVID-19 is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing |
COVID-19 | Doris Duke Charitable Foundation ; Leona M. and Harry B. Helmsley Charitable Trust ; Lyda Hill Philanthropies ; Phrma |
Restricted | DOI:10.17616/R3SB9S, DOI:10.25504/FAIRsharing.uovQrT, DOI:10.25934, r3d100012823 | https://vivli.org/vivli-covid-19-portal-2/, https://doi.org/10.17616/R3SB9S, https://doi.org/10.17616/r3sb9s, https://doi.org/10.25934/, https://dx.doi.org/10.25934/, https://fairsharing.org/10.25504/FAIRsharing.uovQrT, https://doi.org/10.17616/R3SB9S | SCR_018080 | SciCrunch Registry | 2026-11-07 11:58:56 | 1934 | ||||||
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UltraScan Resource Report Resource Website 10+ mentions |
UltraScan (RRID:SCR_018126) | data analysis software, data processing software, software application, software resource | Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis. | Hydrodynamic data, analytical ultracentrifugation experiment, data editing, analysis, sedimentation velocity experiment, spectrum analysis, genetic algorithm, Monte Carlo analysis | Howard Hughes Medical Institute ; NCRR RR 022200 03S1; NCRR RR022200; NIGMS GM120600; NSF ACI 1339649; NSF ANI 228927; NSF DBI 9724273; NSF DBI 9974819; NSF OCI 1032742; NSF TG-MCB 060019T; NSF TG-MCB 070038; NSF TG-MCB 070039; NSF TG-MCB 070040; Robert J. Kleberg Jr. and Helen C. Kleberg Foundation ; San Antonio Life Science Institute |
Free, Available for download, Freely available | SCR_018126 | SciCrunch Registry | 2026-11-07 11:58:56 | 20 | ||||||||||
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HAST Resource Report Resource Website 1+ mentions |
HAST (RRID:SCR_018247) | data analysis software, data processing software, software application, software resource | Software tool for partition stLFR reads based on trio binning using prenatally unique markers. Haplotype resolved assembly for synthetic long reads using Trio-Binning strategy. | Partition stLFR reads, stLFR read, trio binning, haplotype resolved assembly, synthetic long read, reads assembly | Free, Available for download, Freely available | SCR_018247 | SciCrunch Registry | Haplotype-resolved Assembly for Synthetic long reads using a Trio-binning strategy | 2026-11-07 11:58:58 | 1 |
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