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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Bio-Rad: ChemiDoc MP Imaging System Resource Report Resource Website 100+ mentions |
Bio-Rad: ChemiDoc MP Imaging System (RRID:SCR_019037) | instrument resource | Instrument for imaging and analyzing gels and western blots by Bio Rad. Designed to address multiplex fluorescent western blotting, chemiluminescence detection, general gel documentation applications, and stain-free technology imaging needs. | Imaging system, Bio Rad, gel imager, gel imager system, chemiluminescence detection | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019037.pdf | https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000076957.pdf | SCR_019037 | Wester Blot Imaging, ChemiDoc MP Imaging System | 2026-09-05 06:28:45 | 117 | ||||||||
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IDseq Resource Report Resource Website 10+ mentions |
IDseq (RRID:SCR_019038) | analysis service resource, data or information resource, organism-related portal, portal, production service resource, service resource, topical portal | Open source cloud based pipeline and analysis service for metagenomic pathogen detection and monitoring. Hypothesis free global software platform that helps scientists identify pathogens in metagenomic sequencing data. IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes assembly based alignment pipeline which results in assignment of reads and contigs to taxonomic categories. | Metagenomic pathogen detection, metagenomic pathogen monitoring, identify pathogens, metagenomic sequencing data, data analysis | Chan Zuckerberg Initiative | DOI:10.1101/2020.04.07.030551 | Free, Freely available | https://github.com/chanzuckerberg/idseq-workflows/wiki | SCR_019038 | Infectious Disease Sequencing Platform, IDseq Portal | 2026-09-05 06:28:45 | 30 | |||||||
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CLIP Tool Kit Resource Report Resource Website 10+ mentions |
CLIP Tool Kit (RRID:SCR_019034) | CTK | data analysis software, data processing software, software application, software resource, software toolkit | Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer. | CLIP data, data analysis, raw reads, sequencer data generation, genome assemblies, data | has parent organization: Columbia University; New York; USA | Free, Available for download, Freely available | SCR_019034 | 2026-09-05 06:28:45 | 22 | |||||||||
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Agilent MassHunter Qualitative Analysis Resource Report Resource Website 100+ mentions |
Agilent MassHunter Qualitative Analysis (RRID:SCR_019081) | data analysis software, data analytics software, data processing software, software application, software resource | Mass spectrometry screening software for confirmation of target or suspect compounds, and for identification of unknown analytes. Advanced data mining and processing options let find all detectable compounds and confirm targets or identify unknowns. Results can be displayed using data reporting with either preconfigured reports that simplify basic analyses, or completely customized PDF reports. | MassHunter Software, qualitative, mass spectrometry screening, target compound confirmation, unknown analytes identification, data mining, data processing, finding detectable compounds | SCR_019081 | MassHunter Qualitative Analysis | 2026-09-05 06:28:46 | 225 | |||||||||||
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Gilson: Minipuls Evolution peristaltic pump Resource Report Resource Website 1+ mentions |
Gilson: Minipuls Evolution peristaltic pump (RRID:SCR_018955) | instrument resource | Multi channel peristaltic pump for applications with different viscous or abrasive fluids. Allows for channel cartridges, from one to sixteen, to be changed while pump is running. | Perfusion pump, Gilson, multi channel, pump, fluid, channel cartridges, miniplus evolution, instrument, equipment | Restricted | https://www.norlab.com/file/5996/download?token=C7AkKJUp | SCR_018955 | Peristaltic Pump, Perfusion Pump | 2026-09-05 06:28:44 | 4 | |||||||||
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Harvard Apparatus: Single Animal Tabletop Isoflurane Anesthesia System with Small Induction Box Resource Report Resource Website 1+ mentions |
Harvard Apparatus: Single Animal Tabletop Isoflurane Anesthesia System with Small Induction Box (RRID:SCR_018956) | instrument resource | Tabletop anesthesia system suitable for mice, rats and other small animals under 10 lb. Passive scavenging systems. Funnel fill isoflurane vaporizers. | Rat Anesthesia, Mice Anesthesia, Small Animal Anesthesia, anesthesia, tabletop system, isoflurane vaporizer, instrument, equipment | is listed by: USEDit | Restricted | SCR_018956 | Tabletop Anesthesia System, Anesthesia Chamber | 2026-09-05 06:28:44 | 8 | |||||||||
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Ventricular Morphometry Analysis System Resource Report Resource Website |
Ventricular Morphometry Analysis System (RRID:SCR_019007) | VMAS | data analysis software, data processing software, software application, software resource | Software tool to generate whole connected 3D brain ventricular shape model and encode ventricular surface deformation information that is inaccessible by ventricle volume measure. Contains automated segmentation approach and surface based multivariate morphometry statistics. | 3D brain model generation, 3D brain, ventricular shape model, ventricular surface deformation encoding, ventricle volume measure, automated segmentation, multivariate morphometry statistics, analysis system |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Arizona State University; Arizona; USA |
Free, Available for download, Freely available | http://gsl.lab.asu.edu/software/ventricle/ | SCR_019007 | 2026-09-05 06:28:45 | 0 | ||||||||
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E-CRISP Resource Report Resource Website 100+ mentions |
E-CRISP (RRID:SCR_019088) | data access protocol, software resource, web service | Web application to design gRNA sequences. Uses algorithms to identify sgRNA target sequences in any nucleotide sequence for use in CRISPR/Cas mediated genome editing. Used for fast CRISPR target site identification. Enables designing of multiple libraries and creates genome scale libraries for several organisms in few hours. | gRNA sequence design, sgRNA target sequence identification, CRISPR, CRISPR/Cas mediated genome editing, library design, multiple libraries, genome scale libraries, bio.tools |
is listed by: Debian is listed by: bio.tools |
European Research Council Advanced Grant of the European Commission | PMID:24481216 | Free, Freely available | biotools:e-crisp | https://bio.tools/e-crisp | SCR_019088 | 2026-09-05 06:28:46 | 147 | ||||||
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OpenCOR Resource Report Resource Website 1+ mentions |
OpenCOR (RRID:SCR_019001) | simulation software, software application, software resource | Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives. | Modeling environment, reproducible science, CellML format model, CellML format model analysis, CellML format model simulation |
uses: Simulation Experiment Description Markup Language is used by: SPARC Portal |
Free, Available for download, Freely available | SCR_019001 | 2026-09-05 06:28:45 | 6 | ||||||||||
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datasets.datalad.org Resource Report Resource Website 1+ mentions |
datasets.datalad.org (RRID:SCR_019089) | data or information resource, data repository, data set, service resource, storage service resource | DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data. | Version control system, data distribution, super dataset, DataLad dataset, neural data | is related to: DataLad | NIBIB P41 EB019936; NSF 1429999; NSF 1912266 |
Free, Freely available | https://www.datalad.org/datasets.html | SCR_019089 | 2026-09-05 06:28:46 | 8 | ||||||||
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HADDOCK Resource Report Resource Website 100+ mentions |
HADDOCK (RRID:SCR_019091) | data access protocol, simulation software, software application, software resource, web service | Software tool as information driven flexible docking approach for modeling of biomolecular complexes.User friendly integrative modeling of biomolecular complexes.HADDOCK v 2.2 offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in user friendly interface. | Molecular docking, data driven, biomolecular complex, grid computing, hybrid modeling, protein complex | has parent organization: Utrecht University; Utrecht; Netherlands | PMID:12580598 PMID:26410586 |
Restricted | https://www.bonvinlab.org/software/haddock2.2/, https://wenmr.science.uu.nl/haddock2.4/ | SCR_019091 | HADDOCK2.2, HADDOCK2.4, High Ambiguity Driven protein-protein DOCKing | 2026-09-05 06:28:46 | 168 | |||||||
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EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | data access protocol, data or information resource, database, software resource, web service | Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. | Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Warwick; Coventry; United Kingdom |
Biotechnology and Biological Sciences Research Council ; Wellcome Trust |
Restricted | biotools:Enterobase | https://bio.tools/EnteroBase | SCR_019019 | 2026-09-05 06:28:45 | 317 | |||||||
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D-GENIES Resource Report Resource Website 50+ mentions |
D-GENIES (RRID:SCR_018967) | alignment software, data processing software, image analysis software, software application, software resource, standalone software, web application | Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. | bio.tools |
uses: Minimap2 is listed by: Debian is listed by: bio.tools |
PMID:29888139 | Free, Available for download, Freely available | biotools:d-genies | https://github.com/genotoul-bioinfo/dgenies, https://bio.tools/d-genies | SCR_018967 | Dot plot large GENomes in an Interactive, Efficient and Simple way | 2026-09-05 06:28:44 | 56 | ||||||
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Hiroshima University Amphibian Research Center Resource Report Resource Website 10+ mentions |
Hiroshima University Amphibian Research Center (RRID:SCR_019015) | ARC, HUARC | biomaterial supply resource, material resource, organism supplier | Stock center that provides amphibian organisms, frogs and newts, primarily to Japanese investigators. The center runs the National BioResource Project (NBRP) Clawed frogs / Newts, which is financially supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, to distribute these resources. Contributes to maintenance of biologically important strains of frogs and study biological characteristics of amphibian focusing genetics, developmental regulation, speciation, phylogeny, phenotype expression, and environment-induced mutagenesis. | Amphibian, Frog, Xenopus, Newt, Hiroshima University | Ministry of Education ; Culture ; Sports ; Science and Technology (MEXT) |
https://xenopus.nbrp.jp/NBRP_Xenopus/NBRP_X._tropicalis_Top_Page_EN.html | SCR_019015 | Amphibian Research Center, Institute for Amphibian Biology | 2026-09-05 06:28:45 | 10 | ||||||||
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PROSPERO Resource Report Resource Website 1000+ mentions |
PROSPERO (RRID:SCR_019061) | data or information resource, database, narrative resource, standard specification | International database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is health related outcome. Key features from review protocol are recorded and maintained as permanent record. Aims to provide comprehensive listing of systematic reviews registered at inception to help avoid duplication and reduce opportunity for reporting bias by enabling comparison of completed review with what was planned in protocol. | Gold standard authority, registered systematic reviews, reviews in health, reviews in social care, reviews in welfare, reviews in public health, reviews in education, reviews in crime, reviews in justice, reviews in international development, health related outcome, protocol, FASEB list |
is related to: Centre for Reviews and Dissemination has parent organization: University of York, York, England |
NIHR | Free, Freely available | SCR_019061 | 2026-09-05 06:28:46 | 3301 | |||||||||
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Fgenesh plus plus Resource Report Resource Website 1+ mentions |
Fgenesh plus plus (RRID:SCR_018928) | simulation software, software application, software resource | Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software. | Automatic gene prediction, eukaryotic genomes, Softberry software, gene finding | is related to: FGENESH Plus | PMID:16925832 | Restricted | SCR_018928 | Fgenesh Plus Plus, FGENESH plus plus, FGENESH Plus Plus | 2026-09-05 06:28:44 | 7 | ||||||||
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Long Ranger Resource Report Resource Website 10+ mentions |
Long Ranger (RRID:SCR_018925) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants by 10x Genomics. | Analysis pipelines, process chromium sequencing output, align reads, call SNPs, phase SNPs, indel, structural variant, 10x Genomics | Restricted | SCR_018925 | 2026-09-05 06:28:44 | 14 | |||||||||||
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ELDA Resource Report Resource Website 100+ mentions |
ELDA (RRID:SCR_018933) | analysis service resource, data analysis software, data processing software, production service resource, service resource, software application, software resource | Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly. | Limiting dilution analysis, stem cell assay, data set confidence intervals, single hit hypothesis, adequacy test, frequency differences test | is listed by: SoftCite | PMID:19567251 | Free, Freely available | SCR_018933 | Extreme Limiting Dilution Analysis | 2026-09-05 06:28:44 | 463 | ||||||||
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Trinotate Resource Report Resource Website 10+ mentions |
Trinotate (RRID:SCR_018930) | data analysis software, data processing software, software application, software resource, software toolkit | Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. | Automatic functional annotation, transcriptome annotation, de novo assembled transcriptome, model organism, non model organism | Free, Available for download, Freely available | SCR_018930 | Transcriptome Functional Annotation and Analysis | 2026-09-05 06:28:44 | 37 | ||||||||||
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Scayle Resource Report Resource Website |
Scayle (RRID:SCR_019064) | atlas, data or information resource, data repository, data set, portal, service resource, spatially referenced dataset, storage service resource | Open source data platform and multidisciplinary online repository where research groups and different organizations store and make public their datasets, managed by Scayle. Collection of public datasets are available through open.scayle.es and can be reused. NetFlow is network protocol developed by Cisco for collection and monitoring of network traffic flow data generated. Netflow datasets have been used to train machine learning models. | Netflow, DOROTHEA, dataset, network traffic, port scan, training data, traffic flow data | has parent organization: University of Leon, Spain | Free, Freely available, Available for download | https://open.scayle.es/dataset, https://open.scayle.es/dataset/netflow-data-with-sampling-for-test, https://open.scayle.es/dataset/netflow-data-with-sampling-for-training | https://open.scayle.es/dataset/netflow-data, https://open.scayle.es/dataset/netflow-data-without-sampling | SCR_019064 | open.scayle.es | 2026-09-05 06:28:46 | 0 |
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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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