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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ScanITD Resource Report Resource Website 1+ mentions |
ScanITD (RRID:SCR_018886) | data processing software, software application, data analysis software, software resource, sequence analysis software | 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 | Scan Internal Tandem Duplications | 2026-08-15 11:26:02 | 1 | |||||
|
ROSIE Resource Report Resource Website 10+ mentions |
ROSIE (RRID:SCR_018764) | ROSIE | data access protocol, application programming interface, web application, software resource | 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 | NIGMS R01 GM073151; NIGMS R01 GM07822; NIGMS R21 GM102716; NCRR R00 RR024107; NCI U54 CA143907; NEI PN2 EY016586; NIGMS T32 GM 88118; Taiwan Governmental Scholarship for Study Abroad ; Howard Hughes Medical and Institute International Student Research Fellowship ; NSF |
PMID:23717507 | Restricted | https://rosie.rosettacommons.org/ | SCR_018764 | Rosetta Online Server that Includes Everyone | 2026-08-15 11:25:58 | 10 | |||||
|
Chinese Glioma Genome Atlas Resource Report Resource Website 1000+ mentions |
Chinese Glioma Genome Atlas (RRID:SCR_018802) | CGGA | database, topical portal, portal, data or information resource, data set, disease-related 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 | 2026-08-15 11:26:00 | 1344 | ||||||||
|
Random DNA Sequence Generator Resource Report Resource Website 10+ mentions |
Random DNA Sequence Generator (RRID:SCR_018768) | data access protocol, software resource, service 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 | 2026-08-15 11:25:58 | 22 | ||||||||||
|
TRiCoLOR Resource Report Resource Website 1+ mentions |
TRiCoLOR (RRID:SCR_018801) | data processing software, software application, data analysis software, software resource, sequence analysis software | 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 | 2026-08-15 11:25:58 | 2 | ||||||||
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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 | Master-8 EIGHT CHANNEL PROGRAMMABLE PULSE GENERATOR, Master-8 Eight Channel Programmable Pulse Generator | 2026-08-15 11:26:00 | 8 | |||||||||
|
STAMP Resource Report Resource Website 500+ mentions |
STAMP (RRID:SCR_018887) | software toolkit, data processing software, software application, data analysis software, software resource, data visualization software | 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 |
Genome Atlantic ; Natural Sciences and Engineering Research Council of Canada ; Australian Research Council ; Canada Foundation for Innovation ; Canada Research Chairs program ; Dalhousie Faculty of Computer Science ; Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics ; 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 | STAMP v2.1.3, statistical analysis of taxonomic and functional profiles | 2026-08-15 11:25:59 | 588 | |||||
|
GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | data access protocol, software resource, service 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 |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet, https://bio.tools/GOnet | SCR_018977 | 2026-08-15 11:26:00 | 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 | 6 to 600 rpm; 90 to 260 VAC, Masterflex L/S Variable-Speed Digital Drive with Remote I/O | 2026-08-15 11:26:01 | 4 | |||||||||
|
Toolbox for Representational Similarity Analysis Resource Report Resource Website 1+ mentions |
Toolbox for Representational Similarity Analysis (RRID:SCR_019029) | software toolkit, data processing software, software application, data analysis software, software resource | 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 |
UK Medical Research Council ; European Research Council Starting Grant ; European Research Council Advanced Grant |
PMID:24743308 | Free, Available for download, Freely available | SCR_019029 | RSA toolbox | 2026-08-15 11:26:08 | 9 | |||||||
|
Mitoprot Resource Report Resource Website 50+ mentions |
Mitoprot (RRID:SCR_019023) | simulation software, web service, data access protocol, software application, software resource | Web server for prediction of mitochondrial targeting sequences. | Mitochondrial targeting sequence, sequence prediction, mitochondrial sequence, prediction | Free, Freely available | SCR_019023 | 2026-08-15 11:26:07 | 53 | |||||||||||
|
LTRharvest Resource Report Resource Website 10+ mentions |
LTRharvest (RRID:SCR_018970) | simulation software, data processing software, software application, data analysis software, 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 | 2026-08-15 11:26:06 | 47 | |||||||||
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Guide Design Resources Resource Report Resource Website 100+ mentions |
Guide Design Resources (RRID:SCR_018982) | organization portal, data or information resource, laboratory 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 | 2026-08-15 11:26:06 | 353 | ||||||||||
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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://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000076957.pdf | SCR_019037 | Wester Blot Imaging, ChemiDoc MP Imaging System | 2026-08-15 11:26:08 | 117 | |||||||||
|
IDseq Resource Report Resource Website 10+ mentions |
IDseq (RRID:SCR_019038) | topical portal, production service resource, organism-related portal, portal, data or information resource, service resource, analysis service resource | 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 | 2026-08-15 11:26:01 | 30 | |||||||
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CLIP Tool Kit Resource Report Resource Website 10+ mentions |
CLIP Tool Kit (RRID:SCR_019034) | CTK | software toolkit, data processing software, software application, data analysis software, software resource | 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 | 2026-08-15 11:26:08 | 22 | |||||||||
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Agilent MassHunter Qualitative Analysis Resource Report Resource Website 100+ mentions |
Agilent MassHunter Qualitative Analysis (RRID:SCR_019081) | data processing software, software application, data analysis software, data analytics software, 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 | 2026-08-15 11:26:02 | 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 | 2026-08-15 11:26:05 | 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 | 2026-08-15 11:26:05 | 8 | |||||||||
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Ventricular Morphometry Analysis System Resource Report Resource Website |
Ventricular Morphometry Analysis System (RRID:SCR_019007) | VMAS | data processing software, software application, data analysis software, 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 | 2026-08-15 11:26:01 | 0 |
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