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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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CTK Resource Report Resource Website 1+ mentions |
CTK (RRID:SCR_024002) | software resource, software toolkit | Software to support biomedical image computing. | support biomedical image computing, biomedical image computing, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/libctk-dev/ | SCR_024002 | CTK - The Common Tool Kit, ctk | 2026-09-03 05:00:35 | 2 | ||||||||
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NanoLyse Resource Report Resource Website 1+ mentions |
NanoLyse (RRID:SCR_024125) | software library, software resource, software toolkit | Software package to remove reads mapping to the lambda phage genome from a fastq file. | remove reads mapping, lambda phage genome, fastq file, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/nanolyse/ | SCR_024125 | nanolyse | 2026-09-03 05:00:38 | 5 | ||||||||
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libncl Resource Report Resource Website |
libncl (RRID:SCR_024080) | software library, software resource, software toolkit | Software C++ class library for interpreting data files in NEXUS format. NEXUS Class Library software package is collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses.NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored. | interpreting data files in NEXUS format, NEXUS Class Library, phylogenetic analyses, interpreting data files written in NEXUS format, | is listed by: Debian | PMID:14630669 | Free, Available for download, Freely available, | OMICS_20523 | https://sources.debian.org/src/libncl/, https://sources.debian.org/src/ncl/ | SCR_024080 | NCL - the NEXUS Class Library, ncl, NCL | 2026-09-03 05:00:37 | 0 | ||||||
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libqes Resource Report Resource Website |
libqes (RRID:SCR_024083) | software library, software resource, software toolkit | Software C library with bioinformatic focus optimised for speed and clean API. | C library, focus optimised for speed and clean API, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20524 | https://sources.debian.org/src/libqes/ | SCR_024083 | 2026-09-03 05:01:19 | 0 | ||||||||
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NeuroBridge Resource Report Resource Website 1+ mentions |
NeuroBridge (RRID:SCR_023703) | data or information resource, portal, project portal | Platform for data discovery to enhance the reuse of clinical neuroscience and neuroimaging data. Provides NeuroBridge ontology, and combines machine learning with ontology based search of both neuroimaging repositories like XNAT databases and open access full text journals such as PubMed Central. Connects researchers with potential neuroimaging data, by searching text of papers describing neuroimaging studies that contain information on neuroimaging data. | NeuroBridge ontology, ontology based search, searching text, data discovery, clinical neuroscience data, neuroimaging data, data reuse, | Free, Freely available | https://github.com/NeuroBridge | SCR_023703 | 2026-09-03 05:00:14 | 1 | ||||||||||
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The World Factbook Resource Report Resource Website 1+ mentions |
The World Factbook (RRID:SCR_023548) | CIA Factbook | data or information resource, portal | Presents basic realities about world in which we live in and is one of the U.S. Government’s most accessed publications. Provides basic intelligence on history, people, government, economy, energy, geography, environment, communications, transportation, military, terrorism, and transnational issues for 266 world entities. | U.S. Government, publications, basic intelligence, maps, countries, references, CIA, | Free, Freely available, | https://www.cia.gov/the-world-factbook/maps/ | SCR_023548 | 2026-09-03 05:00:46 | 3 | |||||||||
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Multimodal Environment for Neuroimaging and Genomic Analysis Resource Report Resource Website 1+ mentions |
Multimodal Environment for Neuroimaging and Genomic Analysis (RRID:SCR_023822) | MENGA | data or information resource, portal, project portal | Software platform for integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA investigates correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas in order to create comprehensive, integrated data platform. | Allen Human Brain Atlas, imaging data, Allen Human Brain Atlas mRNA data, data integration, | is related to: Allen Institute for Brain Science | PMID:26882227 | Free, Freely available | SCR_023822 | MENGA: Multimodal Environment for Neuroimaging and Genomic Analysis | 2026-09-03 05:00:34 | 1 | |||||||
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medicalterms Resource Report Resource Website |
medicalterms (RRID:SCR_024117) | software library, software resource, software toolkit | Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words. | create specialized dictionaries, medical terms, various languages, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/medicalterms/ | SCR_024117 | hunspell-de-med, wgerman-medical | 2026-09-03 05:00:51 | 0 | ||||||||
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riboWaltz Resource Report Resource Website 10+ mentions |
riboWaltz (RRID:SCR_016948) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates. | calculation, optimal, Psite, offset, diagnostic, analysis, visual, inspection, ribosome, profiling, data, read, alignment, transcript, coordinate |
uses: ggplot2 uses: Biostrings uses: GenomicFeatures uses: GenomicRanges uses: IRanges uses: devtools is related to: R Project for Statistical Computing |
Autonomous Province of Trento ; Wellcome Trust |
PMID:30102689 | Free, Available for download, Freely available | SCR_016948 | 2026-09-03 04:54:20 | 23 | ||||||||
|
Numbers Resource Report Resource Website 1+ mentions |
Numbers (RRID:SCR_016950) | software resource | Software tool to create spreadsheets that include tables and images. You can use Apple Pencil on your iPad to add diagrams and colorful illustrations. | Apple, create, spreadsheet, table, image, diagram, illustration, color | Commercially available | SCR_016950 | 2026-09-03 04:54:08 | 2 | |||||||||||
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Whisker tracking macro Resource Report Resource Website 1+ mentions |
Whisker tracking macro (RRID:SCR_016953) | software resource | ImageJ plugins and macros for whisker tracking. Set of Fiji plugins and macros for tracking a single whisker. | ImageJ, plugin, macro, whisker, tracking, Fiji, single | is a plug in for: ImageJ | Free, Available for download, Freely available | SCR_016953 | 2026-09-03 04:54:12 | 2 | ||||||||||
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Affinity Photo Resource Report Resource Website 10+ mentions |
Affinity Photo (RRID:SCR_016951) | software resource | Software tool for professional photo editing. | Affinity, professional, photo, editing | Commercially available | SCR_016951 | 2026-09-03 04:53:59 | 35 | |||||||||||
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Science Dynamics Resource Report Resource Website 1+ mentions |
Science Dynamics (RRID:SCR_016958) | data or information resource, data set, numeric dataset, portal, project portal | Portal for Science Dynamics projects with open source framework to provide way to query datasets. Code framework, including tutorials for project, titled Over Optimization of Academic Publishing Metrics Observing Goodhart Law in Action, to interactively explore and understand how various properties of journals have changed over time. Datasets, software implementations, code tutorials and interactive web interface for investigating studied networks. | Science, Dynamics, project, dataset, code, framework, optimization, academic, publishing, metric, observing, Goodhart, Law, action, journal, network | has parent organization: University of Washington; Seattle; USA | Microsoft Azure Research Award ; e Washington Re-search Foundation Fund for Innovation in Data-Intensive Discovery ; Moore/Sloan Data Science Environments Project at the University of Washington |
Free, Freely available | https://www.ise.bgu.ac.il/labs/fire/sciencedynamics/index.html | SCR_016958 | 2026-09-03 04:54:09 | 1 | ||||||||
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Olympus: FV1000 Confocal Microscope Resource Report Resource Website 10+ mentions |
Olympus: FV1000 Confocal Microscope (RRID:SCR_016840) | instrument resource | FV1000 confocal laser scanning biological microscope features twin scan system which enables spectroscopy of living intercellular contents and analysis of objects down to a 2nm wavelength resolution. Image size is increased to 4096x4096 pixels. | FV 1000, confocal, laser, scanning, microscope, spectroscopy, living, intercellular, object, Olympus | is provided by: Olympus | Commercially available | http://olympusconfocal.com/brochures/pdfs/FV1000.pdf | SCR_016840 | 2026-09-03 04:54:07 | 20 | |||||||||
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Leica: CM3050 S Research Cryostat Resource Report Resource Website 10+ mentions |
Leica: CM3050 S Research Cryostat (RRID:SCR_016844) | instrument resource | Instrument designed for cryosectioning in biomedical, neuro-anatomical and pharmaceutical research. | instrument, cryosectioning, biomedical, neuroanatomical, cryostat, Leica, histology, equipment | Commercially available | https://www.leicabiosystems.com/sites/default/files/media_product-download/2022-01/Leica_CM3050S_IFU_2v4N_en.pdf | SCR_016844 | Leica CM3050 cryostat | 2026-09-03 04:53:57 | 27 | |||||||||
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HBio: Multichallel Systems: Electro Square Porator ECM 830, BTX Resource Report Resource Website 1+ mentions |
HBio: Multichallel Systems: Electro Square Porator ECM 830, BTX (RRID:SCR_016841) | ECM 830 | instrument resource | ECM 830 is a square wave pulse generator designed for in vitro and in vivo applications for gene, drug and protein delivery for mammalian cells, zebra fish tissue and embryos, nuclear transfer, embryo manipulation, plant protoplast and basic bacteria and yeast transformations. Used in ECM 830 SQUARE WAVE ELECTROPORATION SYSTEM. | BTX, square, wave, pulse, generator, electroporation, ECM 830, transformation | Commercially available | https://drive.google.com/file/d/14QogTk99I1g4bW-H3N9obk7FYhxZbGjr/view?usp=drivesdk | https://www.btxonline.com/media/wysiwyg/tab_content/ECM_830.pdf | SCR_016841 | Electro Square Porator ECM 830, ECM 830, ECM 830 generator | 2026-09-03 04:53:54 | 4 | |||||||
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Illuminating the Druggable Genome Resource Report Resource Website 50+ mentions |
Illuminating the Druggable Genome (RRID:SCR_016924) | IDG | consortium, data or information resource, data repository, organization portal, portal, service resource, storage service resource | Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC). | understudied, target, protein, G protein, coupled, receptor, ion, channel, kinase, bio.tools |
is recommended by: National Library of Medicine is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian |
NIH Common Fund | biotools:pharos | https://pharos.nih.gov/, https://bio.tools/pharos, https://darkmatter.ucsf.edu/about | https://druggablegenome.net | SCR_016924 | Pharos, Illuminating the Druggable Genome, IDG, Illuminating Druggable Genome | 2026-09-03 04:54:08 | 64 | |||||
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Prevention of Lower Urinary Tract Symptoms Resource Report Resource Website |
Prevention of Lower Urinary Tract Symptoms (RRID:SCR_016923) | PLUS | consortium, data or information resource, organization portal, portal | Research consortium from many different fields to plan, perform and analyze the studies that are needed to help researchers conduct future prevention and intervention for Lower Urinary Tract Symptoms (LUTS) in women. | plan, perform, analyze, data, prevent, lower, urinary, track, symptom, women |
is listed by: NIDDK Information Network (dkNET) is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology is related to: University of Minnesota Medical School; Minnesota; USA |
NIDDK | SCR_016923 | Prevention of Lower Urinary Tract Symptoms, Prevention LUTS, PLUS | 2026-09-03 04:54:01 | 0 | ||||||||
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The Human BioMolecular Atlas Program Resource Report Resource Website 10+ mentions |
The Human BioMolecular Atlas Program (RRID:SCR_016922) | HuBMAP | data or information resource, funding resource, portal, project portal | Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows. | organism, cell, tissue, data, generation, technology, organization, functional, mapping, human, body |
uses: Azimuth is listed by: NIDDK Information Network (dkNET) is related to: HuBMAP Data Portal |
NIH | https://humanatlas.io/omap, https://avr.hubmapconsortium.org/, https://commonfund.nih.gov/HuBMAP, https://zenodo.org/records/5244551 | SCR_016922 | Human BioMolecular Atlas Program, HuBMAP, The Human BioMolecular Atlas Program, NIH HuBMAP | 2026-09-03 04:53:57 | 26 | |||||||
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Digital Expression Explorer 2 Project Resource Report Resource Website 1+ mentions |
Digital Expression Explorer 2 Project (RRID:SCR_016929) | DEE2 | data or information resource, data repository, database, portal, project portal, service resource, storage service resource | Software tool as a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive . DEE2 consists of three parts: Webserver where end-users can search for and obtain data-sets of interest, Pipeline that can download and process SRA data as well as users own fastq files, Back-end that collects, filters and organises data provided by contributing worker nodes. | transcriptome, database, RNA-seq, sequencing, processed, data |
is related to: Digital Expression Explorer 2 Source Code is related to: Digital Expression Explorer 2 Docker Image |
DOI:10.5281/zenodo.1561840 | Free, Freely available | SCR_016929 | DEE2 Project | 2026-09-03 04:54:07 | 4 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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