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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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robvis Resource Report Resource Website 100+ mentions |
robvis (RRID:SCR_018755) | robvis | software resource, software toolkit, web application | Software R package and web app, which facilitates rapid production of publication quality risk of bias assessment figures. Used to produce high quality figures that summarize the risk-of-bias assessments performed as part of systematic review or research synthesis project. | Risk of bias assessment, publication figure, publication quality figure, figure production, systematic review, research synthesis project | is related to: Shiny | University Hospitals Bristol NHS Foundation Trust ; University of Bristol |
DOI:10.1002/jrsm.1411 | Free, Freely available | SCR_018755 | SciCrunch Registry | Risk Of Bias VISualization | 2026-11-07 11:59:11 | 100 | ||||||
|
Zeiss: Axio Imager 2 Resource Report Resource Website 10+ mentions |
Zeiss: Axio Imager 2 (RRID:SCR_018876) | instrument resource | Axio Imager 2 resolves samples from tissue sections in pathology to brain specimens in neuroscience to multi dyed FISH specimens. Works with ZEN imaging software. | Upright microscope, Zeiss, imaging microscope, instrument, equipment, upright microscope platform, |
is used by: Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Facility is related to: Zeiss: Axio Imager M2 is related to: Zeiss: Axio Imager Z2m system |
https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018876.pdf | SCR_018856 | https://www.zeiss.com/microscopy/us/products/light-microscopes/axio-imager-2-for-biology.html | SCR_018876 | SciCrunch Registry | Axio Imager 2 | 2026-11-07 11:59:07 | 41 | |||||||
|
T2DSystems Resource Report Resource Website 1+ mentions |
T2DSystems (RRID:SCR_018913) | consortium, data or information resource, disease-related portal, organization portal, portal, project portal, topical portal | Project to bridge gap between in vitro human islet studies and clinical studies in human subjects. Used to integrate cellular and medical research data, collected by partners, with computational modelling to identify pathophysiological mechanisms and markers of spectrum of biological and cellular processes involved in pancreatic beta cell failure leading to impaired glucose tolerance and T2D. | Human islet study, cellular data, medical data, diabetes, pancreatic beta cell failure, impaired glucose tolerance, type 2 diabetes, glucose tolerance | is related to: TIGER Data Portal | Type 2 Diabetes | EU Horizon 2020 | Restricted | SCR_018913 | SciCrunch Registry | Type 2 Diabetes Systems, T2DSystems | 2026-11-07 11:59:07 | 1 | |||||||
|
Diabetic Foot Consortium Resource Report Resource Website |
Diabetic Foot Consortium (RRID:SCR_018914) | DFC | consortium, data or information resource, disease-related portal, organization portal, portal, topical portal | Group of academic institutions committed to studying diabetic foot conditions, such as foot ulcers and wound healing, to develop predictive biomarkers which can be later used to create better treatment plans and improve health and quality of life for people living with diabetes. | Academic institution group, diabetic, diabetic foot, diabetic foot condition, foot ulcer, wound healing, biomarker |
is related to: Indiana University; Indiana; USA is related to: University of Pittsburgh; Pennsylvania; USA is related to: University of Miami; Florida; USA is related to: University of California at San Francisco; California; USA is related to: Stanford University; Stanford; California is related to: University of Michigan; Ann Arbor; USA |
diabetic | NIDDK | SCR_018914 | SciCrunch Registry | 2026-11-07 11:59:00 | 0 | ||||||||
|
ScanITD Resource Report Resource Website 1+ mentions |
ScanITD (RRID:SCR_018886) | data analysis software, data processing software, sequence analysis software, software application, software resource | Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation. | Internal tandem duplication, FLT3, acute myeloid leukemia, TCGA, chimeric alignment, variant allele frequency, variant allele, frequency estimation, , bio.tools |
is listed by: Debian is listed by: bio.tools |
Acute Myeloid Leukemia | DOI:10.5524/100775 | Free, Available for download, Freely available | biotools:ScanItD | https://bio.tools/ScanITD, http://gigadb.org/dataset/100775 | SCR_018886 | SciCrunch Registry | Scan Internal Tandem Duplications | 2026-11-07 11:58:59 | 1 | |||||
|
ROSIE Resource Report Resource Website 10+ mentions |
ROSIE (RRID:SCR_018764) | ROSIE | application programming interface, data access protocol, software resource, web application | Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community. | Web interface for Rosetta, Rosetta online server, Rosetta application serverification, Rosetta user interface | works with: Rosetta | Howard Hughes Medical and Institute International Student Research Fellowship ; NCI U54 CA143907; NCRR R00 RR024107; NEI PN2 EY016586; NIGMS R01 GM073151; NIGMS R01 GM07822; NIGMS R21 GM102716; NIGMS T32 GM 88118; NSF ; Taiwan Governmental Scholarship for Study Abroad |
PMID:23717507 | Restricted | https://rosie.rosettacommons.org/ | SCR_018764 | SciCrunch Registry | Rosetta Online Server that Includes Everyone | 2026-11-07 11:59:11 | 10 | |||||
|
Chinese Glioma Genome Atlas Resource Report Resource Website 1000+ mentions |
Chinese Glioma Genome Atlas (RRID:SCR_018802) | CGGA | data or information resource, data set, database, disease-related portal, portal, topical portal | Web application for data storage and analysis to explore brain tumors datasets from Chinese cohorts. Data portal for storage and interactive exploration of multi-dimensional functional genomic data that includes primary and recurrent glioma samples from Chinese cohorts. Allows users to browse DNA mutation profile, mRNA/microRNA expression profile and methylation profile, and to do correlation and survival analysis in specific glioma subtype. | Functional genomic data, glioma samples, brain tumor datasets, Chinese cohort, whole exome sequencing data, DNA methylation data, mRNA sequencing data, microRNA microarray data, clinical data, DNA mutation profile analysis, expression profile, methylation profile, survival analysis, glioma subtype, FASEB list | Glioma | DOI:10.1101/2020.01.20.911982 | Free, Freely available | SCR_018802 | SciCrunch Registry | 2026-11-07 11:59:12 | 1344 | ||||||||
|
Random DNA Sequence Generator Resource Report Resource Website 10+ mentions |
Random DNA Sequence Generator (RRID:SCR_018768) | data access protocol, service resource, software resource, web service | Web application to generate random DNA sequences. | Random DNA, random DNA sequence, generate random DNA, sequence, generation | is related to: University of California at Irvine; California; USA | Free, Freely available | SCR_018768 | SciCrunch Registry | 2026-11-07 11:59:05 | 22 | ||||||||||
|
TRiCoLOR Resource Report Resource Website 1+ mentions |
TRiCoLOR (RRID:SCR_018801) | data analysis software, data processing software, sequence analysis software, software application, software resource | Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments. | Tandem repeat, long read sequencing data, whole genome alignment, data analysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:tricolor | https://bio.tools/tricolor | SCR_018801 | SciCrunch Registry | 2026-11-07 11:58:57 | 2 | ||||||||
|
A.M.P.I.: Master 8 stimulator Resource Report Resource Website 1+ mentions |
A.M.P.I.: Master 8 stimulator (RRID:SCR_018889) | instrument resource | Pulse generator that can hold 8 different pre-programmed paradigms all of which can use up to all 8 channels. | A.M.P.I, pulse generator, eight channel generator, programmable generator, instrument, equipment | Restricted | https://neurophysics.ucsd.edu/Manuals/Master%208/Master%208%20Eight%20Channel%20Programmable%20Pulse%20Generator.pdf | SCR_018889 | SciCrunch Registry | Master-8 EIGHT CHANNEL PROGRAMMABLE PULSE GENERATOR, Master-8 Eight Channel Programmable Pulse Generator | 2026-11-07 11:59:11 | 8 | |||||||||
|
STAMP Resource Report Resource Website 500+ mentions |
STAMP (RRID:SCR_018887) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups. | Statistical analysis, taxonomic profile, functional profile, metabolic profile, statistical hypothesis test, plot, sample, sample group, sample pair comparison, bio.tools |
is listed by: Debian is listed by: bio.tools |
Australian Research Council ; Canada Foundation for Innovation ; Canada Research Chairs program ; Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics ; Dalhousie Faculty of Computer Science ; Genome Atlantic ; Natural Sciences and Engineering Research Council of Canada ; Tula Foundation Killam Trust |
PMID:25061070 | Free, Freely available | biotools:stamp-metagenomic | https://github.com/dparks1134/STAMP, https://github.com/dparks1134/STAMP/releases, https://bio.tools/stamp-metagenomic | SCR_018887 | SciCrunch Registry | STAMP v2.1.3, statistical analysis of taxonomic and functional profiles | 2026-11-07 11:59:14 | 588 | |||||
|
GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | data access protocol, service resource, software resource, web service | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626; NIGMS ; NIH Common Fund |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet, https://bio.tools/GOnet | SCR_018977 | SciCrunch Registry | 2026-11-07 11:59:13 | 7 | |||||||
|
Cole-Parmer: Masterflex L/S Variable Speed Digital Drive with Remote I/O peristaltic pump Resource Report Resource Website 1+ mentions |
Cole-Parmer: Masterflex L/S Variable Speed Digital Drive with Remote I/O peristaltic pump (RRID:SCR_019028) | instrument resource | Peristaltic pump with flow rate 0.06 to 3400 mL/min, three digit LED display, reversible motor, LED indicators to confirm motor direction and speed range from 6 to 600 rpm. | Pump, reversible motor, peristaltic pump, LED display, variable speed, Perkin Parmer | is listed by: USEDit | Restricted | SCR_019028 | SciCrunch Registry | 6 to 600 rpm; 90 to 260 VAC, Masterflex L/S Variable-Speed Digital Drive with Remote I/O | 2026-11-07 11:59:09 | 4 | |||||||||
|
Toolbox for Representational Similarity Analysis Resource Report Resource Website 1+ mentions |
Toolbox for Representational Similarity Analysis (RRID:SCR_019029) | data analysis software, data processing software, software application, software resource, software toolkit | Software Matlab toolbox to perform representational similarity analysis for neural data. | Representional similarity analysis, data analysis, data, neural data |
is related to: MATLAB has parent organization: University of Cambridge; Cambridge; United Kingdom |
European Research Council Advanced Grant ; European Research Council Starting Grant ; UK Medical Research Council |
PMID:24743308 | Free, Available for download, Freely available | SCR_019029 | SciCrunch Registry | RSA toolbox | 2026-11-07 11:59:03 | 9 | |||||||
|
Mitoprot Resource Report Resource Website 50+ mentions |
Mitoprot (RRID:SCR_019023) | data access protocol, simulation software, software application, software resource, web service | Web server for prediction of mitochondrial targeting sequences. | Mitochondrial targeting sequence, sequence prediction, mitochondrial sequence, prediction | Free, Freely available | SCR_019023 | SciCrunch Registry | 2026-11-07 11:59:03 | 53 | |||||||||||
|
LTRharvest Resource Report Resource Website 10+ mentions |
LTRharvest (RRID:SCR_018970) | data analysis software, data processing software, simulation software, software application, software resource | Software tool for de novo detection of full length LTR retrotransposons in large sequence sets. Delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs. | De novo detection, full length LTR retrotransposons, retrotransposon, large sequence, annotation, sequence length, sequence distance, sequence motif | has parent organization: University of Hamburg; Hamburg; Germany | PMID:18194517 | https://www.zbh.uni-hamburg.de/en/forschung/gi/software/ltrharvest.html | SCR_018970 | SciCrunch Registry | 2026-11-07 11:59:13 | 47 | |||||||||
|
Guide Design Resources Resource Report Resource Website 100+ mentions |
Guide Design Resources (RRID:SCR_018982) | data or information resource, laboratory portal, organization portal, portal | Laboratory portal about research including new approaches for precision gene editing, delivery of molecular and genetic cargo, discovery of novel programmable systems, and engineering of immune system to develop next generation of therapeutics. Provides collection of tools for guide design.CRISPR.MIT.EDU of Guide Design Tools is no longer available, documented on August 28,2020. | Guide desin tools, precision gene editing, immune system engineering, next generation therapeutics, guide design | has parent organization: Broad Institute | Free, Freely available | SCR_018982 | SciCrunch Registry | 2026-11-07 11:59:17 | 353 | ||||||||||
|
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 | SciCrunch Registry | Wester Blot Imaging, ChemiDoc MP Imaging System | 2026-11-07 11:59:18 | 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 | SciCrunch Registry | Infectious Disease Sequencing Platform, IDseq Portal | 2026-11-07 11:59:14 | 30 | |||||||
|
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 | SciCrunch Registry | 2026-11-07 11:59:09 | 22 |
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