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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Human Cell Atlas Resource Report Resource Website 100+ mentions |
Human Cell Atlas (RRID:SCR_016530) | atlas, catalog, data or information resource, database, image, map, portal | Software tool as a catalog of comprehensive reference of human cells based on their stable properties, transient features, locations and abundances. Map to show the relationships among its elements. Open data international collaborative project involving diverse scientific communities to provide a framework for understanding cellular dysregulation in human disease. | human, cell, line, atlas, catalog, map, open, data, international, project, FASEB list |
is listed by: NIDDK Information Network (dkNET) is related to: Optimus Pipeline is related to: Smart-seq2 Multi-Sample Pipeline is related to: Broad Institute Genomics Platform |
PMID:29206104 | Free, Available for download, Freely available | SCR_016530 | SciCrunch Registry | 2026-11-07 11:58:42 | 127 | |||||||||
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Tests for deviation from Hardy-Weinberg equilibrium Resource Report Resource Website 10+ mentions |
Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) | data analysis software, data processing software, software application, software resource | Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases. | deviation, Hardy-Weinberg, equilibrium, test, association, population, genetic, identify, susceptibility, gene, disease, single, nucleotide, polymorphisms, snp, allele | SCR_016496 | SciCrunch Registry | 2026-11-07 11:58:18 | 18 | ||||||||||||
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Cardiovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) | data or information resource, database, disease-related portal, portal, topical portal | Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data. | genetic, data, cardiovascular, disease, human | is listed by: NIDDK Information Network (dkNET) | cardiovascular disease, myocardial infarction, atrial fibrillation | Accelerating Medicines Partnership in Type 2 Diabetes ; National Institute of Cardiovascular Diseases and Stroke |
Free, Available for download, Google ID required, Tutorial available | SCR_016536 | SciCrunch Registry | 2026-11-07 11:58:18 | 31 | ||||||||
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jPerfusionModule Resource Report Resource Website 1+ mentions |
jPerfusionModule (RRID:SCR_016534) | data analysis software, data processing software, image analysis software, software application, software resource | Software tool written in Java that reads DICOM-files from Dynamic Susceptibility Contrast (DSC) Magnetic Resonance Imaging (MRI) and calculates standardized Time-to-Peak (stdTTP) parameter. Maps from this calculation are provided as RGB- and Monochrom2-Dicom files and may be sent to a PACS automatically. Works on windows® platforms on PC’s (Intel® CPUs from Pentium I up to the I7-octo cores) together with the Philips 1.5T ACS-NT up to the Ingenia Systems (n> 20.000), with the Philips 3.0T Systems (n ~ 1.000), the Siemens 1.5T Avanto (SQ-machine) (n> 10.000) and the Siemens 3.0T TimTrio (n ~ 200) so far. Works with uncompressed DICOM-standard files. | dictom, file, read, dynamic, susceptibility, constrast, mangentic, resonance, imaging, calculate, standardized, stdTTP, parameter, | Commercially available | SCR_016534 | SciCrunch Registry | 2026-11-07 11:58:38 | 1 | |||||||||||
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VoxBlast Resource Report Resource Website 1+ mentions |
VoxBlast (RRID:SCR_016491) | 3d visualization software, data processing software, data visualization software, image processing software, software application, software resource | Software application for science and medicine which offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering for any 3-D data. It accepts stacks of registered 2-D images and creates 3-D projections from any viewpoint. | VayTek Inc., 3D, image, data, visualisation, reconstruction, measurement, projection, science, medicine |
is listed by: OMICtools has parent organization: University of Iowa Labs and Facilities |
Commercially available, Free demo version available | SCR_016491 | SciCrunch Registry | 2026-11-07 11:58:28 | 1 | ||||||||||
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nonparametricGGC_toolbox Resource Report Resource Website 1+ mentions |
nonparametricGGC_toolbox (RRID:SCR_016539) | nonparametricGGC | data analysis software, data processing software, software application, software resource | Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions. | nonparametric, Granger, causality, simulation, framework, code, estimate, brain, function | is related to: MATLAB | the Swiss National Science Foundation | Free, Available for download, Freely available | SCR_016539 | SciCrunch Registry | nonparametric Granger Geweke Causality | 2026-11-07 11:58:29 | 2 | |||||||
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NetworkUnit Resource Report Resource Website 1+ mentions |
NetworkUnit (RRID:SCR_016543) | software library, software resource, software toolkit | Library of a test driven framework for formally validating scientific models against experimental data used for validation testing of spiking neuron network simulations on the network activity level. | validation, neuroscience, electrophysiology, spiking, neural, network, simulation |
uses: Neo uses: Elephant is related to: SciUnit is related to: NeuronUnit |
Free, Available for download, Freely available | SCR_016543 | SciCrunch Registry | 2026-11-07 11:58:42 | 6 | ||||||||||
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HARP Resource Report Resource Website 1+ mentions |
HARP (RRID:SCR_016546) | 3d visualization software, data processing software, data visualization software, image processing software, software application, software resource, standalone software | Software as a cross platform application for automating the processing of μCT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release. | MRC Harwell UK, automating, processing, uCT, OPT, image, data | is related to: International Mouse Phenotyping Consortium (IMPC) | Free, Available for download, Freely available | harp.exe | SCR_016546 | SciCrunch Registry | 2026-11-07 11:58:38 | 1 | |||||||||
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VPV Resource Report Resource Website 1+ mentions |
VPV (RRID:SCR_016545) | VPV | 3d visualization software, data processing software, data visualization software, software application, software resource | Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph. | Phyton, desktop, 3D viewer, analysis, results, phenotype, detection, LAMA pipeline | is listed by: International Mouse Phenotyping Consortium (IMPC) | Free, Available for download, Freely available | SCR_016545 | SciCrunch Registry | Volume Phenotype Viewer, volume phenotype viewer | 2026-11-07 11:58:29 | 1 | ||||||||
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DCC Resource Report Resource Website 1+ mentions |
DCC (RRID:SCR_016544) | DCC | data analysis software, data processing software, software application, software resource | Software tool as an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations and large-scale annotation efforts. | databases, sequencing experiments, sequencing annotation, data annotation | Free, Available for download, Freely available | SCR_016544 | SciCrunch Registry | Data Coordination Center | 2026-11-07 11:58:18 | 1 | |||||||||
|
RNA22 Resource Report Resource Website 100+ mentions |
RNA22 (RRID:SCR_016507) | RNA22 | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases. | pattern, based, detecting, microRNA, binding, site, complex, sequence, genome, analysis, FASEB list | is listed by: OMICtools | A Star ; Singapore ; NIDDK DK04763; NIH AI54973 |
Free, Available for download, Freely available | SCR_016507 | SciCrunch Registry | RiboNucleic Acid 22 | 2026-11-07 11:58:37 | 222 | |||||||
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CajaDB Resource Report Resource Website 1+ mentions |
CajaDB (RRID:SCR_016506) | data or information resource, database, software resource, web application | Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network. | marmoset, data, genomic, expression, alternative, splicing, animal, model, neuropsychiatry, social, behavior, ontology, protein, network | Amazonas State Research Support Foundation ; Brain Institute ; Brazilian Council for Research and Technological Development ; Federal University of Rio Grande do Norte ; Multidisciplinary Environment ; NPAD/UFRN |
Free, Freely available | SCR_016506 | SciCrunch Registry | 2026-11-07 11:58:28 | 1 | ||||||||||
|
DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | SciCrunch Registry | Drug target Interaction Network Inference Engine based on Supervised analysis | 2026-11-07 11:58:18 | 6 | ||||
|
Jpred Resource Report Resource Website 100+ mentions |
Jpred (RRID:SCR_016504) | data analysis software, data analytics software, data processing software, sequence analysis software, software application, software resource | Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions. | protein, secondary, structure, prediction, amino, acid, sequence, accurate, JNet algorithm, solvent, accessibility, coiled, coil, region | Biotechnology and Biological Sciences Research Council ; Wellcome Trust 106370Z14; Wellcome Trust 355804783; Wellcome Trust WT083481; Wellcome Trust WT092340 |
DOI:10.1093/nar/gkn238 | Free, Available for download, Freely available,Tutorial available | SCR_016504 | SciCrunch Registry | Jprotein secondary structure PREDiction | 2026-11-07 11:58:41 | 133 | ||||||||
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miRmap Resource Report Resource Website 100+ mentions |
miRmap (RRID:SCR_016508) | data analytics software, software application, software library, software resource, software toolkit | Software application as an open source Pyton library to search and predict miRNA targets. | search, predict, miRNA, target | is listed by: OMICtools | Swiss Institute of Bioinformatics ; Swiss National Science Foundation |
PMID:23034802 | Free, Available for download, Freely available, Tutorial available | http://cegg.unige.ch/mirmap | SCR_016508 | SciCrunch Registry | 2026-11-07 11:58:42 | 227 | |||||||
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MIMMS microscope 1.0 (2016) Resource Report Resource Website 1+ mentions |
MIMMS microscope 1.0 (2016) (RRID:SCR_016511) | MIMMS | instrument resource | Modular platform for performing two‐photon laser scanning microscopy (TPLSM) optimized for in vivo applications. | instrument, computer, controlled, microscope, two, photon, laser, scanning, imagining | has parent organization: Howard Hughes Medical Institute | Available for Free for non profit research in the Janelia research community | SCR_016511 | SciCrunch Registry | Modular In vivo Multiphoton Microscopy System | 2026-11-07 11:58:29 | 7 | ||||||||
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NAT/NCS2 Hound Resource Report Resource Website 1+ mentions |
NAT/NCS2 Hound (RRID:SCR_016473) | NAT, NCS2 | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins. | protein, sequence, scan, identify, evolutionary, classify, prokaryotic, nucleobase, transporter, protein, amino acid, conserved |
is listed by: OMICtools has parent organization: University of Thessaly; Thessaly; Greece |
DOI:10.1101/332452 | Free, Available to download, Freely available | SCR_016473 | SciCrunch Registry | Nucleobase Ascorbate Transporter, NCS2:Nucleobase Cation Symporter 2 | 2026-11-07 11:58:17 | 1 | |||||||
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MetaPGN Resource Report Resource Website 1+ mentions |
MetaPGN (RRID:SCR_016472) | MetaPGN | data analysis software, data processing software, data visualization software, network graph visualization software, software application, software resource, software toolkit | Pipeline for construction and graphical visualization of annotated pangenome networks from microbial genomes. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data provides pangenome analysis to uncultured microbial taxa., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | construct, graphical, visualization, annotated, pangenome, network, microbal, genome, metagenome | PMID:30277499 | THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/peng-ye/MetaPGN | SCR_016472 | SciCrunch Registry | Meta PanGeNome | 2026-11-07 11:58:41 | 2 | |||||||
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Thermo Fisher: Nanodrop 1000 Spectrophotometer Resource Report Resource Website 50+ mentions |
Thermo Fisher: Nanodrop 1000 Spectrophotometer (RRID:SCR_016517) | instrument resource | Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution. | ABRF, spectrophotometer, nanodrop, concentration measurement, optical density, DNA, RNA, protein, nanodrop, instrument, equipment |
is listed by: USEDit works with: Thermo Scientific NanoDrop 1000 Software |
Commercially available | https://drive.google.com/file/d/1C1Dj_A1QxQibucCbFNues9EDZebDnx8K/view?usp=drivesdk | SCR_018035, Model_Number_Nanodrop_1000, SCR_020560 | https://www.marshallscientific.com/Nanodrop-ND-1000-Spectrophotometer-p/nd-1000.htm, https://www.selectscience.net/products/nanodrop-1000-spectrophotometer/?prodID=79482#tab-2, http://tools.thermofisher.com/content/sfs/manuals/nd-1000-v3.8-users-manual-8%205x11.pdf | SCR_016517 | SciCrunch Registry | NanoDrop 1000, Nanodrop ND-1000, Thermo Scientific NanoDrop 1000, NanoDrop 1000 Spectrophotometer | 2026-11-07 11:58:37 | 89 | ||||||
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PNNsMiceMachineVision Resource Report Resource Website 1+ mentions |
PNNsMiceMachineVision (RRID:SCR_016485) | PNNsMiceMachineVision | data or information resource, database, software application, software resource, source code | Data and code (Python) related to research paper: V. Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera "Cocaine-induced preference conditioning: a machine vision perspective". | data, code, Phyton, research, paper, probabilistic, neural, network | Free, Available for download, Freely available | SCR_016485 | SciCrunch Registry | Probabilistic Neural Networks MiceMachineVision | 2026-11-07 11:58:28 | 2 |
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