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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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Agilent: 7890/5975 GC/MS system Resource Report Resource Website 1+ mentions |
Agilent: 7890/5975 GC/MS system (RRID:SCR_018695) | instrument resource | Agilent GC/MS is single quadrupole instrument with electron ionization. GC/MS runs under ChemStation open access software, and trained open access users select from menu of standard methods to analyze their samples. | Agilent GC/MS, quadrupole instrument, electron ionization, ChemStation software, sample analyzer, 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_018695.pdf | https://www.agilent.com/cs/library/usermanuals/public/G3170-90036.pdf | SCR_018695 | SciCrunch Registry | Agilent 7890/5975 GC/MS | 2026-10-10 12:40:57 | 1 | ||||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NCATS UL1 TR001425; NCI T32 CA236764; NHLBI U54 HL127624; NIEHS P30 ES006096; NIGMS U01 GM120953; NIMH R01 MH107487 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | SciCrunch Registry | 2026-10-10 12:40:18 | 4 | ||||||||
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Qiagen: PyroMark Q96 System Resource Report Resource Website 10+ mentions |
Qiagen: PyroMark Q96 System (RRID:SCR_018617) | instrument resource | Sequencing and quantification platform for epigenetics, mutation gene expression analysis, and microbial identification and resistance typing. With its 96-well format, automatic base-calling function, and dedicated software solutions for methylation analysis and assay design. | Pyrosequencer, Instrument, Equipment, Qiagen, USEDit, ABRF | is listed by: USEDit | SCR_020413, Model_Number_Q96 | SCR_018617 | SciCrunch Registry | 2026-10-10 12:40:17 | 11 | ||||||||||
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Rigaku: Alchemist II Liquid Handler Resource Report Resource Website |
Rigaku: Alchemist II Liquid Handler (RRID:SCR_018625) | instrument resource | Liquid handling system for production of complex liquid formulations produced from individual stock solutions of various chemical and liquid properties. With a CV of less than 2%. | Rigaku, Liquid Handler, Instrument Equipment, USEDit | is listed by: USEDit | SCR_019564, Model_Number_Alchemist_II | SCR_018625 | SciCrunch Registry | 2026-10-10 12:40:17 | 0 | ||||||||||
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rVista Resource Report Resource Website 10+ mentions |
rVista (RRID:SCR_018707) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites. | Noncoding sequence, regulatory potential analysis, matrices search, TRANSFAC library collection, cis regulatory element, process alignment, zPicture, blastz, pairwise alignment, genome, analysis, transcription factor binding site, bio.tools |
is listed by: Debian is listed by: bio.tools works with: TRANSFAC |
PMID:15215384 | Free, Freely available | biotools:rvista | https://bio.tools/rvista | SCR_018707 | SciCrunch Registry | rVista 2.0 | 2026-10-10 12:40:57 | 34 | ||||||
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FunCoup Resource Report Resource Website 1+ mentions |
FunCoup (RRID:SCR_018711) | data access protocol, data or information resource, database, service resource, software resource, web service | Database of genome wide functional coupling networks. Provides tools to explore predicted networks and to retrieve detailed information about data underlying each prediction. Web service for functional coupling search. | Genome, genome functional coupling network, coupling network, functional coupling, functional couplings search, gene identifier, genome data | has parent organization: Karolinska Institute; Stockholm; Sweden | Stockholm University ; Swedish Research Council |
PMID:24185702 | Free, Freely available | SCR_018711 | SciCrunch Registry | 2026-10-10 12:40:19 | 3 | ||||||||
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NGScloud2 Resource Report Resource Website 1+ mentions |
NGScloud2 (RRID:SCR_018716) | data analysis software, data processing software, software application, software resource | Software tool for RNA-seq analysis of non model species using cloud computing. Provides user friendly front end to operate Amazon hardware resources and to control workflows of bioinformatic analysis of de novo RNA-seq, reference-based RNA-seq and functional annotation specifically oriented to plant species. | RNAseq analysis, non model species, cloud computing, AWS, spot instances, RNAseq, RADseq, functional annotation, plant | Amazon Research Grant ; Spanish Ministry of Economy and Competitiveness ; Spanish National Parks Agency Ministry of Agriculture |
PMID:29726914 | Free, Available for download, Freely available | https://github.com/GGFHF/NGScloud/ | SCR_018716 | SciCrunch Registry | NGScloud | 2026-10-10 12:40:19 | 1 | |||||||
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Thermo Fisher: GeneAtlas System Resource Report Resource Website 1+ mentions |
Thermo Fisher: GeneAtlas System (RRID:SCR_018715) | instrument resource | System for processing Affymetrix microarrays. Microarray analysis system. Includes array strip and hybridization assembly, Fluidics station, Imaging station. | ABRF, Affymetrix, instrument, Thermo Fisher Scientific, Affymetrix Gene Atlas Fluidics Station, Affymetrix HuGene, Geneatlas system, imaging station, equipment |
is listed by: USEDit works with: Affymetrix Transcriptome Analysis Console Software works with: Affymetrix Transcriptome Analysis Console Software |
https://assets.thermofisher.com/TFS-Assets/LSG/brochures/geneatlas_system_brochure.pdf | SCR_018715 | SciCrunch Registry | GeneAtlas System, Affymetrix GeneAtlas System | 2026-10-10 12:40:19 | 1 | |||||||||
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Thermo Fisher: NanoDrop 8000 Spectrophotometer Resource Report Resource Website 1+ mentions |
Thermo Fisher: NanoDrop 8000 Spectrophotometer (RRID:SCR_018600) | instrument resource | Microvolume UV Vis spectrophotometer for nucleic acid and protein quantification that can measure multiple samples using 1 to 2 uL of samples. Can analyze spectrum of 220nm to 750nm and measure 96 samples in less than six minutes. Can measure multiple samples in one measurement cycle, up to eight samples at one time. Has single sample mode. Can analyze the full spectrum from 220 to 750nm and calculates sample purity ratios 260/280. | Spectrophotometer, Instrument, Equipment, Nanodrop, USEDit, ABRF |
is listed by: USEDit is related to: Thermo Fisher: NanoDrop Lite Spectrophotometer |
Commercially available | Model_Number_NanoDrop_8000, SCR_020315 | https://afns-labs.ualberta.ca/wp-content/uploads/sites/58/2018/05/Nanodrop-ND-8000-brochure.pdf.pdf | SCR_018600 | SciCrunch Registry | 2026-10-10 12:40:17 | 7 | ||||||||
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PRISMA Resource Report Resource Website 1000+ mentions |
PRISMA (RRID:SCR_018721) | PRISMA | data or information resource, narrative resource, portal, standard specification | Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions. | MDAR, standard, report standard, reporting reviews, randomized trial, evaluating randomized trial, reporting systematic review, intervention evaluation, meta analysis | is listed by: SoftCite | Ottawa Hospital Research Institute ; University of Oxford |
Free, Freely available | SCR_018721 | SciCrunch Registry | Preferred Reporting Items for Systematic Reviews and Meta-Analyses | 2026-10-10 12:40:19 | 1593 | |||||||
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CONSORT Resource Report Resource Website 100+ mentions |
CONSORT (RRID:SCR_018720) | CONSORT | data or information resource, narrative resource, organization portal, portal, standard specification | Standards for transparent trials reporting. Encompasses various initiatives developed by CONSORT Group to alleviate problems arising from inadequate reporting of randomized controlled trials. Main product of CONSORT is CONSORT Statement, which is evidence based, minimum set of recommendations for reporting randomized trials. CONSORT Statement is endorsed by medical journals and leading editorial organizations. | MDAR, standard, transparent trial, trial reporting, CONSORT group, controlled trial, CONSORT Statement, randomized trials reporting, medical journal, editorial organization, reporting | is related to: CONSORT TM | Family Health International ; Medical Research Council ; Ottawa Hospital Research Institute ; University of Oxford |
Free, Freely available | SCR_018720 | SciCrunch Registry | Consolidated Standards of Reporting Trials | 2026-10-10 12:40:25 | 389 | |||||||
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Monocle3 Resource Report Resource Website 100+ mentions |
Monocle3 (RRID:SCR_018685) | data analysis software, data processing software, software application, software resource, software toolkit | Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. | Data analysis, singel cell RNAseq data, single cell RNAseq experiment, transcriptome dynamics | has parent organization: University of Washington; Seattle; USA | NHGRI P50 HG006193; NIGMS P01 GM099117; NIH Office of the Director DP2 0D008514; NIH Office of the Director DP2 OD00667; Single Cell Genomics initiative |
PMID:24658644 | Free, Available for download, Freely available | https://github.com/cole-trapnell-lab/monocle3 | SCR_018685 | SciCrunch Registry | Monocle, Monocle 3 | 2026-10-10 12:40:18 | 342 | ||||||
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Nikon: AZ100 Confocal Microscope Resource Report Resource Website 1+ mentions |
Nikon: AZ100 Confocal Microscope (RRID:SCR_018603) | instrument resource | Nikon Instruments AZ100 C1si is macro confocal microscope system combining stereo and compound microscopes into single hybrid imaging system for dynamic imaging of single cells or whole specimens.System covers range of magnifications from 5x to 400x. Has triple nosepiece that can switch magnifications. AZ100 C1si boasts simultaneous 32 channel spectral image acquisition over spectral range of 320 nm in single scan. Simultaneous 32 channel acquisition at 10 nm, 5 nm or 2.5 nm bandwidths, all software controlled, is possible. | Confocal Microscope, Instrument, Equipment, Nikon, USEDit, ABRF | is listed by: USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018603.pdf | Model_Number_AZ100, SCR_020325 | https://www.mvi-inc.com/wp-content/uploads/AZ100-Manual.pdf | SCR_018603 | SciCrunch Registry | 2026-10-10 12:40:23 | 2 | |||||||
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MicroFilePlus Resource Report Resource Website 1+ mentions |
MicroFilePlus (RRID:SCR_018724) | data processing software, image processing software, software application, software resource | Software tool as microscopy image file format converter by MBF Bioscience. Converts common microscopy image files to JPEG2000 and OME-TIFF. Used to view, analyze, and share big image data from many sources. | Image file format, image converter, converter, OME-TIFF Format, jpeg2000, jpx, JP2, MBF Bioscience | Restricted | SCR_018724 | SciCrunch Registry | MicroFilePlus, MicroFile+, microfileplus | 2026-10-10 12:40:19 | 2 | ||||||||||
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Marshall Scientific: MJ Research PTC-100 PCR Thermocycler Resource Report Resource Website 10+ mentions |
Marshall Scientific: MJ Research PTC-100 PCR Thermocycler (RRID:SCR_018602) | instrument resource | Thermocycler that operates with 96 well and 60 well microplates. Has temperature configurations from 0 C to 105 C and pressure and height adjustment via thumbwheel. Comes with 14 pre-programmed protocols. | PCR Thermocycler, Instrument, Equipment, USEDit, MJ Research, ABRF | is listed by: USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018602.pdf | Model_Number_PTC100, SCR_020292 | https://www.artisantg.com/info/MJ_PTC_100_Manual.pdf | SCR_018602 | SciCrunch Registry | 2026-10-10 12:40:56 | 12 | |||||||
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Waters: 2695 HPLC System Resource Report Resource Website 1+ mentions |
Waters: 2695 HPLC System (RRID:SCR_018649) | instrument resource | High performance liquid chromatographic system with quaternary, low pressure mixing pump and inline vacuum degassing. It has wavelengths of 190 to 800 nm and flow rates from 50 uL per min to 5 mL per min with 2.1 mm ID columns and larger. Autosampler has maximum capacity of 120 vials (12x32, 2 mL) with programmable temperature control from 4 to 40C. Heated column compartment provides temperatures from 5 degrees above ambient to 65C. | HPLC System, Instrument, Equipment, USEDit, Waters, ABRF | is listed by: USEDit | Commercially available | Model_Number_2695, SCR_020877 | https://www.waters.com/webassets/cms/library/docs/720004547en.pdf | SCR_018649 | SciCrunch Registry | Waters Alliance 2695 Separations Module | 2026-10-10 12:40:24 | 1 | |||||||
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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 | 2026-10-10 12:40:24 | 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 | 2026-10-10 12:40:56 | 0 | |||||||
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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 | 2026-10-10 12:40:18 | 1 | |||||||||
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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 | 2026-10-10 12:40:57 | 3 |
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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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