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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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QoRTs Resource Report Resource Website 10+ mentions |
QoRTs (RRID:SCR_018665) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R. | Quality control, data processing, RNAseq data, DNAseq data, analysis, data management, error detection, biases, artifacts, high throughput sequencing technology, | NHGRI | PMID:26187896 | Free, Freely available | https://github.com/hartleys/QoRTs | SCR_018665 | SciCrunch Registry | 2026-10-10 12:40:57 | 27 | ||||||||
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Preseq Resource Report Resource Website 10+ mentions |
Preseq (RRID:SCR_018664) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries. | Genome, high throughput sequencing, predicting library complexity, distinct yield prediction, genomic library, initial sequencing experiment, molecular complexity prediction, sequencing libraryb, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:23435259 | Free, Freely available | biotools:preseq | https://github.com/smithlabcode/preseq, https://bio.tools/preseq | SCR_018664 | SciCrunch Registry | 2026-10-10 12:40:18 | 21 | |||||||
|
Thermo Fisher: QE-HFX mass spectrometer Resource Report Resource Website 10+ mentions |
Thermo Fisher: QE-HFX mass spectrometer (RRID:SCR_018703) | instrument resource | HFX offers scanning rate to improve proteomic depth for discovery applications. Integrates well with targeted applications such as parallel reaction monitoring. Mass Spectrometer to identify and quantify proteins, peptides, lipids, glycans and small molecules accurately. | Thermo Scientific, Mass Spectrometer, small molecules identification, small molecules quantification, Instrument, Equipment, USEDit | is used by: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018703.pdf | Model_Number_QE-HFX | https://assets.thermofisher.com/TFS-Assets/CMD/Specification-Sheets/PS-64048-LC-MS-Q-Exactive-HF-Orbitrap-PS64048-EN.pdf | https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFALGMBFZ#/IQLAAEGAAPFALGMBFZ | SCR_018703 | SciCrunch Registry | Thermo QE-HFX, Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer | 2026-10-10 12:40:57 | 11 | ||||||
|
Thermo Fisher: Orbitrap Fusion nanoLC/MS system Resource Report Resource Website 1+ mentions |
Thermo Fisher: Orbitrap Fusion nanoLC/MS system (RRID:SCR_018702) | instrument resource | System includes Thermo Orbitrap Fusion Tribrid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments. | Thermo Orbitrap Fusion Tribrid mass spectrometer, Waters M-Class Acquity nanoUPLC, instrument, equipment, USEDit | is used by: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility | https://tools.thermofisher.com/content/sfs/brochures/PS-63844-LC-MS-Orbitrap-Fusion-PS63844-EN.pdf | SCR_018702 | SciCrunch Registry | Thermo Orbitrap Fusion nanoLC/MS, Orbitrap Fusion nanoLC/MS | 2026-10-10 12:40:19 | 4 | |||||||||
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Thermo Fisher: LTQ XL LC/MS system Resource Report Resource Website |
Thermo Fisher: LTQ XL LC/MS system (RRID:SCR_018701) | instrument resource | LTQ XL ion trap mass spectrometer with Agilent 1100 HPLC system for metabolite identification, stability testing, degradation products, and high abundance quantitation. | LTQ XL ion trap, mass spectrometer, Agilent 1100 HPLC, metabolite identification, stability testing, degradation product, high abundance quantitation, equipment, instrument, USEDit | is used by: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility | https://www.pragolab.cz/documents/LTQ_XL_PS1.pdf | SCR_018701 | SciCrunch Registry | Thermo LTQ XL LC/MS | 2026-10-10 12:40:19 | 0 | |||||||||
|
Discrete Morse Resource Report Resource Website |
Discrete Morse (RRID:SCR_018662) | DM | data processing software, image processing software, software application, software resource | Discrete Morse based pipeline for neuron tracing on tracer injection and single neuron data sets. Automatically generates set of trees summarization of given neuron imaging data. Used to extract tree skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections. | Neuron tracing, tracer injection, single neuron data set, set of trees summarization generation, neuron image data, extract individual neuron tree skeleton, volumetric brain image data, summarize collection, tracer injection labelled neuron | DOI:10.1101/2020.03.21.000323v1 | Free, Freely available | SCR_018662 | SciCrunch Registry | DiscreteMorse | 2026-10-10 12:40:18 | 0 | ||||||||
|
minet Resource Report Resource Website |
minet (RRID:SCR_018661) | data analysis software, data processing software, network analysis software, software application, software resource, software toolkit | Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data. | Inferring transcriptional network, mutual information, gene network, microarray data, gene, statistical dependencies model, gene to gene interaciton, statistical quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor has parent organization: Free University of Brussels; Brussels; Belgium |
Communaute Francaise de Belgique | PMID:18959772 | Free, Available for download, Freely available | biotools:minet | http://minet.meyerp.com/, https://bio.tools/minet | SCR_018661 | SciCrunch Registry | Mutual Information NETworks | 2026-10-10 12:40:24 | 0 | |||||
|
MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | data access protocol, service resource, software resource, web service | Web service for querying or retrieving gene annotation data. | Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCATS UL1 TR001114; NCI K22 CA188163; NHGRI U01 HG006476; NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; Scripps Translational Science Institute |
DOI:10.1186/s13059-016-0953-9 | Free, Freely available | biotools:mygene.info, BioTools:mygene.info | https://bio.tools/mygene.info, https://bio.tools/mygene.info, https://bio.tools/mygene.info | SCR_018660 | SciCrunch Registry | 2026-10-10 12:40:57 | 34 | ||||||
|
Stratagene: 1800 UV Crosslinker Resource Report Resource Website |
Stratagene: 1800 UV Crosslinker (RRID:SCR_018631) | instrument resource | UV crosslinker designed to crosslink DNA or RNA to nylon, nitrocellulose, or nylon reinforced nitrocellulose membranes in 25 to 50 seconds. It is equipped with internal photodetector to compensate for aging ultraviolet bulbs. | Crosslinker, Instrument, Equipment, USEDit, ABRF, Stratagene | is listed by: USEDit | Commercially available | Model_Number_1800, SCR_020532 | https://ipmb.sinica.edu.tw/microarray/index.files/Stratalinker%20UV%20Crosslinker.pdf | SCR_018631 | SciCrunch Registry | 2026-10-10 12:40:56 | 0 | ||||||||
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SCIEX: 4000 QTRAP Mass Spectrometer Resource Report Resource Website |
SCIEX: 4000 QTRAP Mass Spectrometer (RRID:SCR_018630) | instrument resource | Hybrid triple quadrupole linear ion trap mass spectrometer for drug discovery and development, metabolite identification, contaminant testing, proteomic applications, post translationally modified proteins discovery, protein identification, and biomarker validation. | Mass Spectrometer, Instrument, Equipment, USEDit, Sciex, ABRF | is listed by: USEDit | Commercially available | SCR_020508, Model_Number_Sciex_4000_QTRAP | https://collateral.sciex.com/manuals/4000-qtrap-hardware-guide/4000-qtrap-hardware-guide.pdf | SCR_018630 | SciCrunch Registry | 2026-10-10 12:40:17 | 0 | ||||||||
|
TA Instruments: Electroforce 3200 Mechanical Testing Apparatus Resource Report Resource Website 1+ mentions |
TA Instruments: Electroforce 3200 Mechanical Testing Apparatus (RRID:SCR_018637) | instrument resource | Mechanical testing apparatus with 225 N or 450 N maximum force and range of static to 300 Hz frequency response. Tests include torsion testing, creep under dynamic loading, special environment hot cold chambers, biomedical research, and engineered materials test applications.. | Mechanical Testing Apparatus, Instrument, Equipment, USEDit, ABRF | is listed by: USEDit | SCR_019752, Model_Number_3200 | https://www.tainstruments.com/wp-content/uploads/ElectroForce_Test_Instruments.pdf | SCR_018637 | SciCrunch Registry | TA Instruments Electroforce 3200 Series Mechanical Testing Apparatus | 2026-10-10 12:40:17 | 2 | ||||||||
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Roche: Ventana Discovery XT Immunohistochemistry Processor Resource Report Resource Website 1+ mentions |
Roche: Ventana Discovery XT Immunohistochemistry Processor (RRID:SCR_018643) | instrument resource | Immunohistochemistry processor that can be used for immunohistochemistry and in situ hybridization slide preparation and processing. | Immunohistochemistry Processor, Ventana | is listed by: USEDit | Model_Number_Ventana_Discovery_XT | SCR_018643 | SciCrunch Registry | 2026-10-10 12:40:18 | 6 | ||||||||||
|
Thermo Fisher: Arcturus Cellect Laser Capture Microdissection System Resource Report Resource Website 100+ mentions |
Thermo Fisher: Arcturus Cellect Laser Capture Microdissection System (RRID:SCR_018641) | instrument resource | Laser capture microdissection system that includes infrared lasers. It can be used for laser capture microdissection LCM, ultraviolet UV laser cutting, sanger sequencing, next generation sequencing, and quantitative PCR. | Arcturus, Laser Capture Microdissection System, Instrument Equipment, USEDit | is listed by: USEDit | Model_Number_XT, SCR_019580 | https://assets.thermofisher.com/TFS-Assets/CSD/Specification-Sheets/Arcturus_Cellect_SpecSheet.pdf | SCR_018641 | SciCrunch Registry | 2026-10-10 12:40:24 | 215 | |||||||||
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Thermo Fisher: Cytomat 6001 Automated Wide Range Incubator Resource Report Resource Website |
Thermo Fisher: Cytomat 6001 Automated Wide Range Incubator (RRID:SCR_018646) | instrument resource | Automated wide range incubator used to minimize plate movement, receive samples, store plates, and track plates.Temperature range is from 10 to 50 degrees Celsius with humidity level of up to 95 rH. | Automated Wide Range Incubator, Instrument, Equipment, USEDit, Thermo Scientific, ABRF | is listed by: USEDit | SCR_020541, Model_Number_Cytomat 6001 | https://www.artisantg.com/info/Kendro_Cytomat_6000_6001_Manual.pdf | SCR_018646 | SciCrunch Registry | 2026-10-10 12:40:18 | 0 | |||||||||
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Leica: SP8 DIVE multi photon microscope Resource Report Resource Website 1+ mentions |
Leica: SP8 DIVE multi photon microscope (RRID:SCR_018852) | SP8 DIVE | instrument resource | Multiphoton confocal microscope with spectrally tunable detection. Equipped with 4Tune, tunable, non descanned detection unit. | Multiphoton microscope, microscope, confocal microscope, Leica microscope, 4Tune, tunable, instrument, equipment | is listed by: USEDit | Restricted | https://www.uu.se/download/18.3e997b3218a92fdae6a1c553/1695042166717/c_600184-l_1-k_leica-sp8-dive-manual---biovis.pdf | SCR_018852 | SciCrunch Registry | SP8 Deep In Vivo Explorer | 2026-10-10 12:40:21 | 2 | |||||||
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TIMER Resource Report Resource Website 1000+ mentions |
TIMER (RRID:SCR_018737) | TIMER | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features. | Tumor, tumor infiltrating immune cell, immune cell, cell, analysis, cancer cell, cancer type, tumor immunological feature, tumor genomic feature, display | Dana-Farber Cancer Institute ; National Natural Science Foundation of China ; NCI CA180980 |
PMID:29092952 | Free, Freely available | SCR_018737 | SciCrunch Registry | Tumor IMmune Estimation Resource | 2026-10-10 12:40:19 | 3010 | |||||||
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Imspector Resource Report Resource Website 50+ mentions |
Imspector (RRID:SCR_018863) | data analysis software, data processing software, software application, software resource | Software tool for real time analysis and data visualization. Software system for experimental control and quantitative data analysis in microscopy and spectroscopy.Integration of data processing and acquisition allows real time analysis and visualization of experimental results. | Data analysis, real time data, visualization, quantitative analysis, microscopy, spectroscopy | Free, Freely available | https://github.com/AbberiorInstruments/ImspectorDocs/blob/master/docs/intro.rst, https://imspector.abberior-instruments.com/ | SCR_018863 | SciCrunch Registry | 2026-10-10 12:40:59 | 85 | ||||||||||
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Repetier Host Resource Report Resource Website 10+ mentions |
Repetier Host (RRID:SCR_018901) | 3d visualization software, data processing software, data visualization software, software application, software resource | Open source 3D printing software which supports multi part printing and has slicers. | 3D printing, multi part printing support, slicer, data visualization, 3D visualization | Free, Available for download, Freely available | SCR_018901 | SciCrunch Registry | Repetier-Host | 2026-10-10 12:40:22 | 41 | ||||||||||
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Sutter: Movable Objective Microscope Resource Report Resource Website 1+ mentions |
Sutter: Movable Objective Microscope (RRID:SCR_018860) | MOM | instrument resource | Two photon microscope capable of imaging deep within living specimens when combined with Ti:Sapphire Laser. Provides 3D objective movement and rotation allowing specimen to remain stationary. | Sutter Instruments, two photon microscope, imaging, living specimen, 3D objective movement, 3D objective rotation, stationary speciment, custom design, instrument, equipment, microscope | is listed by: USEDit | Restricted. | SCR_018860 | SciCrunch Registry | Movable Objective Microscope (MOM), Sutter MOM | 2026-10-10 12:40:21 | 5 | ||||||||
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TRACESPipe Resource Report Resource Website 1+ mentions |
TRACESPipe (RRID:SCR_018831) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as hybrid pipeline for reconstruction and analysis of viral and host genomes at multi-organ level. Pipeline for identification, assembly, and analysis of viral genomes, that combine DNA sequence data from multiple organs. Cooperation between compression based prediction, sequence alignment, and de-novo assembly. Provides transmission and storage of data. | Hybrid pipeline, genome reconstruction, genome analysis, viral genome, host genome, multi organ sequencing, multi organ level, DNA sequence data, multiple organ data, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.5524/100771 | Free, Freely available | biotools:tracespipe | http://dx.doi.org/10.5524/100771, https://bio.tools/tracespipe | SCR_018831 | SciCrunch Registry | 2026-10-10 12:40:58 | 2 |
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