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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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SigCom LINCS Resource Report Resource Website 1+ mentions |
SigCom LINCS (RRID:SCR_022275) | data access protocol, software resource, web service | Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures. | FAIR data, data and metadata search engine, gene expression signatures, gene expression signature processed, analyzed, and visualized, LINCS, GTEx, GEO, gene expression signatures, | NHLBI U54HL127624; NIDDK R01DK131525; NIH Office of the Director OT2OD030160 |
PMID:35524556 | Free, Freely available | https://github.com/MaayanLab/sigcom-lincs | SCR_022275 | SigCom Library of Integrated Network-based Cellular Signatures | 2026-09-05 06:30:12 | 8 | |||||||
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KineFold Resource Report Resource Website 1+ mentions |
KineFold (RRID:SCR_022273) | data access protocol, software resource, web service | Web service for RNA/DNA folding predictions including pseudoknots and entangled helices.Used for prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. | RNA secondary structure, minimum free energy prediction, RNA/DNA folding predictions, pseudoknots and entangled helices, pseudoknots in RNA structures, clustered stochastic simulations | has parent organization: Curie Institute; Paris; France | French Ministry of Higher Education | PMID:14676318 | Free, Freely available | SCR_022273 | 2026-09-05 06:30:12 | 4 | ||||||||
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HEXplorer score Resource Report Resource Website 1+ mentions |
HEXplorer score (RRID:SCR_022269) | data access protocol, software resource, web service | Web tool for genomic HEXploring allows landscaping of novel potential splicing regulatory elements. Allows landscaping of splicing regulatory regions, provides quantitative measure of mutation effects on splice enhancing and silencing properties and permitts calculation of mutationally most effective nucleotide. | Predicts splicing potential, splicing regulatory regions, mutation effects on splice enhancing and silencing properties | German Research Foundation | DOI:10.1093/nar/gku736 | Free, Freely available | SCR_022269 | 2026-09-05 06:30:12 | 6 | |||||||||
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%MinMax Resource Report Resource Website 1+ mentions |
%MinMax (RRID:SCR_022268) | data access protocol, software resource, web service | Software tool for calculating and comparing synonymous codon usage and its impact on protein folding. Used to harmonize codon usage frequencies for heterologous gene expression. Codon usage calculator that evaluates relative usage frequencies of synonymous codons used to encode protein sequence of interest and compares these results to rigorous null mode.Evaluates synonymous codon usage patterns for any coding sequence from any fully sequenced genome. | Calculating and comparing synonymous codon usage, impact on protein folding, harmonize codon usage frequencies, heterologous gene expression, codon usage calculator, encode protein sequence | has parent organization: University of Notre Dame; Indiana; USA | PMID:29090506 | Free, Freely available | SCR_022268 | 2026-09-05 06:30:13 | 2 | |||||||||
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HiCRes Resource Report Resource Website 1+ mentions |
HiCRes (RRID:SCR_022319) | simulation software, software application, software resource | Software pipeline to estimate and predict genomic resolution of Hi-C libraries. Used for estimating and predicting HiC library resolution. | Hi-C libraries, 3D chromatin interactions genome wide measurement, estimate resolution of dataset, genomic resolution | NEI ZIAEY000450; NEI ZIAEY000546 |
DOI:10.1093/nar/gkab1235 | Free, Available for download, Freely available | https://github.com/ClaireMarchal/HiCRes | SCR_022319 | 2026-09-05 06:30:13 | 1 | ||||||||
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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 | 2026-09-05 06:30:13 | 50 | ||||||
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University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility Resource Report Resource Website 10+ mentions |
University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility (RRID:SCR_022410) | CyTOF | access service resource, core facility, material storage repository, service resource, storage service resource | CyTOF�enables multi-parametric high-dimensional single�cell analysis�of more than 40 markers per cell, with�minimal background and compensation�issues.�Core�offers variety of�CyTOF-related services including�reagent distribution, consultation,�antibody conjugation, and data acquisition.� | USEDit, ABRF, stockroom | is listed by: ABRF CoreMarketplace | ARBF_1419 | https://coremarketplace.org?citation=1&FacilityID=1419 | SCR_022410 | University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center, IFI CyTOF Service Center | 2026-09-05 06:30:14 | 39 | |||||||
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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 | Last (Meta)Genomic Assembler Standing | 2026-09-05 06:30:12 | 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 | 2026-09-05 06:30:14 | 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 | PROTAC diastereomer Design negative control | 2026-09-05 06:30:12 | 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 | PROTAC Design based on Bioinformatics | 2026-09-05 06:30:12 | 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 | 2026-09-05 06:30:14 | 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 | Linker Design and Optimization | 2026-09-05 06:30:12 | 0 | |||||||||
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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 | 2026-09-05 06:30:14 | 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 | Single Nucleotide Polymorphisms-sites | 2026-09-05 06:30:12 | 3 | |||||||||
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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 | 2026-09-05 06:30:12 | 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 | Nucleofector 2b Device | 2026-09-05 06:30:12 | 7 | |||||||||
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University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility Resource Report Resource Website 10+ mentions |
University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility (RRID:SCR_022415) | PMBB | access service resource, biobank, core facility, material storage repository, service resource, storage service resource | BioBank supports researchers by providing centralized access to large number of annotated blood and tissue samples. | USEDit, ABRF, annotated blood and tissue samples | is listed by: ABRF CoreMarketplace | ARBF_1421 | https://coremarketplace.org?citation=1&FacilityID=1421 | SCR_022415 | University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank | 2026-09-05 06:30:14 | 16 | |||||||
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EZcalcium Resource Report Resource Website 1+ mentions |
EZcalcium (RRID:SCR_022354) | data analysis software, data processing software, software application, software resource | Software package for MATLAB that makes motion correction, segmentation, signal extraction and dimension reduction, analysis, and visualization of calcium imaging data easy to implement. Open source toolbox for analysis of calcium imaging data. | OpenBehavior, neural signal analysis, neural recording, optical imaging, analyze calcium imaging data |
is listed by: OpenBehavior has parent organization: David Geffen School of Medicine at UCLA; California; USA |
DOI:10.3389/fncir.2020.00025 | Free, Available for download, Freely available | https://github.com/porteralab/EZcalcium | SCR_022354 | 2026-09-05 06:30:13 | 3 | ||||||||
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GuPPy Resource Report Resource Website 10+ mentions |
GuPPy (RRID:SCR_022353) | data analysis software, data processing software, software application, software resource | Software Python toolbox that makes fiber photometry data analysis intuitive and light on programming.Used to measure neural activity of freely behaving animals. | OpenBehavior, photometry analysis, neural activity measure, freely behaving animals |
is listed by: OpenBehavior has parent organization: Northwestern University Feinberg School of Medicine; Illinois; USA |
DOI:10.1038/s41598-021-03626-9 | https://github.com/LernerLab/GuPPy | SCR_022353 | Guided Photometry Analysis in Python | 2026-09-05 06:30:13 | 18 |
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