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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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BpForms Resource Report Resource Website |
BpForms (RRID:SCR_018653) | data access protocol, software resource, software toolkit, web service | Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. | Molecular structure description, DNA, RNA, protein, modification, epigenetics, transcriptomics, post transcriptional modification, post translational modification, bio.tools |
uses: BcForms is used by: ObjTables is used by: Datanator is listed by: Debian is listed by: bio.tools is related to: BcForms is related to: ObjTables |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bpforms | https://bio.tools/bpforms | SCR_018653 | SciCrunch Registry | 2026-10-24 12:48:00 | 0 | ||||||
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ObjTables Resource Report Resource Website |
ObjTables (RRID:SCR_018652) | data management software, data processing software, software application, software resource, software toolkit | Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort. | Creating reusable dataset, combining spreadsheet with schema, spreadsheet, table, supplementary material, schema, object relational map, validation, bio.tools |
uses: BpForms uses: BcForms is listed by: bio.tools is listed by: Debian is related to: BpForms |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
Free, Freely available | biotools:objtables | https://bio.tools/objtables | SCR_018652 | SciCrunch Registry | 2026-10-24 12:48:00 | 0 | |||||||
|
trend Resource Report Resource Website 1+ mentions |
trend (RRID:SCR_018658) | data analysis software, data processing software, software application, software resource, software toolkit | Software package includes tests for trends and change points detection. Used in analysis of environmental data. | tests for trend detection, environmental data analysis, Cox-Stuart Trend Test, Mann-Kendall Trend Test, Hirsch-Slack Test, partial Pearson and Spearman correlation trend test, change-point detection | is related to: CRAN | Free, Freely available | SCR_018658 | SciCrunch Registry | Non-Parametric Trend Tests and Change-Point Detection | 2026-10-24 12:48:01 | 1 | |||||||||
|
McKinley: Cellometer Auto 2000 Cell Viability Counter Resource Report Resource Website 1+ mentions |
McKinley: Cellometer Auto 2000 Cell Viability Counter (RRID:SCR_018656) | instrument resource | Cell viability counter. Touchscreen fluorescent automated cell counter for primary samples by Nexcelom Bioscience. | Cell viability counter, touchscreen cell counter, fluorescent automated cell counter, Nexcelom Bioscience, instrument, equipment | is related to: USEDit | Restricted | https://biotech.gsu.edu/core/Documents/Manuals/Cellometer2000.pdf | SCR_018656 | SciCrunch Registry | 2026-10-24 12:48:01 | 3 | |||||||||
|
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 | 2026-10-24 12:48:01 | 27 | ||||||||
|
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 | 2026-10-24 12:48:01 | 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 | 2026-10-24 12:48:01 | 11 | ||||||
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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 | 2026-10-24 12:48:01 | 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 | 2026-10-24 12:48:01 | 0 | |||||||||
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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 | 2026-10-24 12:48:01 | 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 | 2026-10-24 12:48:01 | 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 | 2026-10-24 12:48:01 | 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 | 2026-10-24 12:48:00 | 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 | 2026-10-24 12:48:00 | 0 | ||||||||
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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 | 2026-10-24 12:48:00 | 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 | 2026-10-24 12:48:00 | 6 | ||||||||||
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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 | 2026-10-24 12:48:00 | 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 | 2026-10-24 12:48:00 | 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 | 2026-10-24 12:48:03 | 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 | 2026-10-24 12:48:02 | 3010 |
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