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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CORAL Resource Report Resource Website 50+ mentions |
CORAL (RRID:SCR_022711) | CORAL | data analysis software, data processing software, software application, software resource | Software tool as framework for rigorous self validated data modeling and integrative, reproducible data analysis. | FAIR data, Contexton, Microtype, Data Management, Provenance, Data Analysis, Jupyter | has parent organization: University of California at Berkeley; Berkeley; USA | US Department of Energy | Free, Available for download, Freely available | SCR_022711 | SciCrunch Registry | Contextual Ontology based Repository Analysis Library | 2026-09-26 02:17:21 | 95 | |||||||
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OptiType Resource Report Resource Website 50+ mentions |
OptiType (RRID:SCR_022279) | data analysis software, data processing software, software application, software resource | Software tool for precision HLA typing from next generation sequencing data. | Precision HLA typing, next generation sequencing data, HLA typing, NGS data |
is listed by: Debian is listed by: OMICtools |
German Federal Ministry of Education and Research ; German Research Foundation |
PMID:25143287 | Free, Available for download, Freely available | OMICS_05461 | https://sources.debian.org/src/optitype/ | SCR_022279 | SciCrunch Registry | 2026-09-26 02:17:18 | 50 | ||||||
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SNPRelate Resource Report Resource Website 10+ mentions |
SNPRelate (RRID:SCR_022719) | data analysis software, data processing software, software application, software resource | Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data. | parallel computing, relatedness and principal component analysis, SNP data analysis | NHGRI U01 HG 004446 | PMID:23060615 | Free, Available for download, Freely available | https://github.com/zhengxwen/SNPRelate | SCR_022719 | SciCrunch Registry | 2026-09-26 02:17:21 | 13 | ||||||||
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LMAS Resource Report Resource Website 1+ mentions |
LMAS (RRID:SCR_022251) | data processing software, image analysis software, image reconstruction software, software application, software resource | Automated workflow enabling benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. Results are presented in interactive HTML report where selected global and reference specific performance metrics can be explored. | Shotgun metagenomics, genomic assembler | has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel | Free, Available for download, Freely available | SCR_022251 | SciCrunch Registry | Last (Meta)Genomic Assembler Standing | 2026-09-26 02:17:18 | 1 | |||||||||
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Knowledge based Identification of Pathway Enzymes Resource Report Resource Website 1+ mentions |
Knowledge based Identification of Pathway Enzymes (RRID:SCR_022370) | KIPEs | data analysis software, data processing software, software application, software resource | Software tool as automatic approach for identification of players in biosynthesis pathway. Used for automatic annotation of flavonoid biosynthesis steps in new transcriptome of genome sequence assembly. Various enzymes of entire metabolic networks can be identified if sufficient knowledge about functionally relevant amino acids is available.Combines comprehensive sequence similarity analyses with inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. | Automatic annotation, biosynthesis steps, new transcriptome of genome sequence assembly annotation, biosynthesis pathway, sequence similarity analyses, inspection of functionally relevant amino acid residues, peptide sequences | PMID:32867203 | Free, Available for download, Freely available | SCR_022370 | SciCrunch Registry | 2026-09-26 02:17:20 | 2 | |||||||||
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BOC Sciences PROTAC diastereomer Design negative control Service Resource Resource Report Resource Website |
BOC Sciences PROTAC diastereomer Design negative control Service Resource (RRID:SCR_022249) | service resource | Service to design PROTAC diastereomer to meet new drug discovery goals. | BOC Sciences, biomedical service, PROTAC, diastereomer design, negative control | has parent organization: BOC Sciences | Restricted | SCR_022249 | SciCrunch Registry | PROTAC diastereomer Design negative control | 2026-09-26 02:17:19 | 0 | |||||||||
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BOC Sciences PROTAC Design based on Bioinformatics Resource Report Resource Website |
BOC Sciences PROTAC Design based on Bioinformatics (RRID:SCR_022248) | service resource | Provides PROTAC design based on bioinformatics services to customers to meet new drug discovery goals. Used for analysis of large scale multi group data to discover potential drug targets based on biological network characteristics, multi gene chip, proteome, metabolome data. | BOC Sciences, biomedical service, target drug availability prediction, drug side effects prediction, new drug discovery | has parent organization: BOC Sciences | Restricted | SCR_022248 | SciCrunch Registry | PROTAC Design based on Bioinformatics | 2026-09-26 02:17:18 | 0 | |||||||||
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Pediatric Cancer Data Commons Resource Report Resource Website 1+ mentions |
Pediatric Cancer Data Commons (RRID:SCR_022369) | PCDC | data or information resource, disease-related portal, portal, topical portal | PCDC brings together clinical, genomic, and imaging data from institutions around the world to transform pediatric cancer research and outcomes. Headquartered at University of Chicago, PCDC works with international leaders in pediatric cancers and National Cancer Institute to develop and apply uniform data standards that facilitate collection, combination, and analysis of data from many different sources. PCDC Consortium developes common core data dictionary and common governance structure spanning pediatric cancers neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, and Hodgkin lymphoma to enable innovative cross disease research as well as set standard for future cancer data commons endeavors. | pediatric cancer, clinical data, genomic data, imaging data, uniform data standards, common core data dictionary, common governance structure, | is related to: University of Chicago; Illinois; USA | pediatric cancer, neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, Hodgkin lymphoma | Free, Freely available | SCR_022369 | SciCrunch Registry | 2026-09-26 02:17:19 | 2 | ||||||||
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BOC Sciences Linker Design and Optimization Services Service Resource Resource Report Resource Website |
BOC Sciences Linker Design and Optimization Services Service Resource (RRID:SCR_022247) | service resource | Provides Linker Design and Optimization services to meet new drug discovery goals. | BOC Sciences, biomedical service, linker design and optimization | has parent organization: BOC Sciences | Restricted | SCR_022247 | SciCrunch Registry | Linker Design and Optimization | 2026-09-26 02:17:18 | 0 | |||||||||
|
multiHiCcompare Resource Report Resource Website 1+ mentions |
multiHiCcompare (RRID:SCR_022368) | data analysis software, data processing software, software application, software resource | Software package for removing biases across multiple Hi-C datasets. Properly handles Hi-C-specific decay of chromatin interaction frequencies with increasing distance between interacting regions. | detecting priori known chromatin interaction differences, jointly normalized datasets, recover loss of chromatin interactions, Hi-C specific decay of chromatin interaction frequencies, remove bias between multiple Hi-C datasets | American Cancer Society ; NIEHS T32ES007334 |
DOI:10.1093/bioinformatics/btz048 | Free, Available for download, Freely available | https://github.com/dozmorovlab/multiHiCcompare | SCR_022368 | SciCrunch Registry | 2026-09-26 02:17:19 | 4 | ||||||||
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SNP-sites Resource Report Resource Website 1+ mentions |
SNP-sites (RRID:SCR_022265) | data analysis software, data processing software, software application, software resource | Software tool to find SNP sites from multi-FASTA alignment file. Can output results in multiple formats for downstream analysis. | find SNP sites, Single Nucleotide Polymorphisms, single nucleotide polymorphisms extracting, large whole genome alignment, | Free, Available for download, Freely available | https://github.com/sanger-pathogens/snp-sites | SCR_022265 | SciCrunch Registry | Single Nucleotide Polymorphisms-sites | 2026-09-26 02:17:19 | 3 | |||||||||
|
Zeiss: LSM 900 with Airyscan 2 Resource Report Resource Website 10+ mentions |
Zeiss: LSM 900 with Airyscan 2 (RRID:SCR_022263) | instrument resource | Laser scanning confocal microscope for multiplex imaging and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Laser scanning, confocal microscope, imaging and analysis, microscope, instrument, equipment, USEDit | is listed by: USEDit | THIS RESOURCE IS NO LONGER IN SERVICE | Model_Number_LSM _900 | SCR_022263 | SciCrunch Registry | 2026-09-26 02:17:18 | 15 | |||||||||
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Lonza: Nucleofector 2b Device Resource Report Resource Website 1+ mentions |
Lonza: Nucleofector 2b Device (RRID:SCR_022262) | instrument resource | System for efficient transfection of a variety of hard-to transfect cell lines and primary cells. Using certified aluminium electrode cuvettes this single cuvette system is capable of transfecting various substrates in a low throughput format. | Lonza, transfection of hard to transfect cells, cell lines, primary cells, transfection | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_022262.pdf | SCR_022262 | SciCrunch Registry | Nucleofector 2b Device | 2026-09-26 02:17:18 | 7 | |||||||||
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University of Toyama; Toyama; Japan Resource Report Resource Website |
University of Toyama; Toyama; Japan (RRID:SCR_022751) | university | Japanese national university in Toyama Prefecture established in 1949. University of Toyama has three campuses, namely Gofuku, Sugitani, and Takaoka campuses. | is parent organization of: USVCAM | SCR_022751 | SciCrunch Registry | 2026-09-26 02:17:22 | 0 | ||||||||||||
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RefSeq non-redundant proteins Resource Report Resource Website 50+ mentions |
RefSeq non-redundant proteins (RRID:SCR_022748) | data or information resource | Non-redundant RefSeq protein records are currently provided for archaeal and bacterial RefSeq genomes, with exception of selected reference genomes, by NCBI prokaryotic genome annotation pipeline. This scope definition may change in the future to include additional RefSeq sub-kingdoms or other organism groups and some GenBank conceptual translation protein records may provide cross-links to RefSeq non-redundant proteins. | NIH, NLM, Non-redundant RefSeq protein records, RefSeq protein records, NCBI prokaryotic genome annotation, protein records |
is related to: RefSeq is related to: RefSeqGene |
Free, Freely available | SCR_022748 | SciCrunch Registry | 2026-09-26 02:17:22 | 55 | ||||||||||
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OrthoVenn2 Resource Report Resource Website 100+ mentions |
OrthoVenn2 (RRID:SCR_022504) | data access protocol, software resource, web service | Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences. | whole genome comparison and annotation, orthologous clusters across multiple species, identify orthologous gene clusters, comparing multiple species protein sequences | National Natural Science Foundation of China | PMID:31053848 | Free, Freely available | SCR_022504 | SciCrunch Registry | 2026-09-26 02:17:20 | 288 | |||||||||
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PavCA project Resource Report Resource Website 1+ mentions |
PavCA project (RRID:SCR_022508) | PavCA | data or information resource, portal, topical portal | Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates. | Behavior, behavior analysis, Pavlovian conditioning, apparatus, Pavlovian conditioned approach, Instrument, OpenBehavior |
is listed by: OpenBehavior has parent organization: University at Buffalo; New York; USA |
Free, Freely available | SCR_022508 | SciCrunch Registry | Pavlovian Conditioned Approach, PavCA | 2026-09-26 02:17:20 | 2 | ||||||||
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Surgisphere Resource Report Resource Website |
Surgisphere (RRID:SCR_022759) | organization | American healthcare analytics company established in 2008. Originally textbook marketing company, it came under scrutiny in May 2020 after it had provided large datasets of COVID-19 patients which were subsequently found to be extremely unreliable. The questionable data was used in studies published in The Lancet and The New England Journal of Medicine in May 2020. On 15 June 2020, company website was taken offline. | medical records, healthcare analytics company, unreliable datasets | SCR_022759 | SciCrunch Registry | 2026-09-26 02:17:22 | 0 | ||||||||||||
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ExonScan Web Server Resource Report Resource Website 1+ mentions |
ExonScan Web Server (RRID:SCR_022516) | data access protocol, software resource, web service | Software framework for modeling sequence motifs based on maximum entropy principle. | modeling sequence motifs, maximum entropy principle | has parent organization: MIT; Cambridge; Massachusetts; United States | PMID:15285897 | Free, Freely available | SCR_022516 | SciCrunch Registry | ExonScan | 2026-09-26 02:17:20 | 2 | ||||||||
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ShinyCell Resource Report Resource Website 10+ mentions |
ShinyCell (RRID:SCR_022756) | data processing software, data visualization software, software application, software resource | Software R package to create interactive Shiny based web applications to visualise single cell data via visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots, visualising composition of different clusters / groups of cells using proportion plots and visualising expression of multiple genes using bubbleplots / heatmap.Shiny Interactive Web Apps for Single-Cell Data. | visualise single cell data, visualising cell information, gene expression on reduced dimensions, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information | works with: Shiny | Free, Available for download, Freely available | SCR_022756 | SciCrunch Registry | 2026-09-26 02:17:22 | 24 |
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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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