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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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DrivAER Resource Report Resource Website 1+ mentions |
DrivAER (RRID:SCR_019076) | data analysis software, data processing software, software application, software resource | Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data. | Manifold interpretation, scRNAseq data, relevance scores infering, transcriptional program, psuedotemporal ordering, disease status, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:drivaer | https://bio.tools/drivaer | SCR_019076 | SciCrunch Registry | Driving transcriptional programs using AutoEncoder based Relevance scores | 2026-10-10 12:41:57 | 1 | |||||||
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STENCIL Resource Report Resource Website 1+ mentions |
STENCIL (RRID:SCR_021878) | data processing software, data visualization software, software application, software resource | Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise. | Visualizing genomic data, sharing genomic data, interactive genomic data visualizations, interpret sequencing data | NIEHS ES013768; NIGMS GM125722 |
DOI:10.1101/2021.06.04.447108 | Free, Available for download, Freely available | SCR_021878 | SciCrunch Registry | 2026-10-10 12:41:55 | 4 | |||||||||
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IMGT HighV-QUEST Resource Report Resource Website 10+ mentions |
IMGT HighV-QUEST (RRID:SCR_018196) | alignment software, analysis service resource, data or information resource, data processing software, image analysis software, portal, production service resource, service resource, software application, software resource | Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. | Next generation sequencing, B cell, T cell, sequence alignment, immunoglobulin, antibody, T cell receptor, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian |
CNRS ; GENCI ; MESR ; NHMRC ; Université Montpellier 2 ; France |
PMID:22647994 PMID:23995877 PMID:22665256 |
Restricted | biotools:IMGt_HighV-QUESt | https://bio.tools/IMGT_HighV-QUEST | SCR_018196 | SciCrunch Registry | IMGT/HighV QUEST, IMGT/HighV-QUEST, IMGT web portal | 2026-10-10 12:41:54 | 15 | |||||
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Genomic Association Tester Resource Report Resource Website 10+ mentions |
Genomic Association Tester (RRID:SCR_020949) | GAT | data analysis software, data processing software, simulation software, software application, software resource | Software tool as simulation framework for testing association of genomic intervals. Used for estimating significance of overlap between multiple sets of genomic intervals. Estimates statistical significance based on simulation and controls for multiple tests using false discovery rate. | Genomic intervals, genomic intervals association testing, overlap significance estimation, genomic intervals sets, segment length distribution, chromosomal location, isochores | UK Medical Research Council | PMID:23782611 | Free, Available for download, Freely available | https://github.com/AndreasHeger/gat | http://code.google.com/p/genomic-association-tester | SCR_020949 | SciCrunch Registry | 2026-10-10 12:41:57 | 31 | ||||||
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PM4NGS Resource Report Resource Website 1+ mentions |
PM4NGS (RRID:SCR_019164) | data analysis software, data management software, data processing software, software application, software resource, software toolkit, workflow software | Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution. | NGS workflow, standard organizational structure generation, Next Generation Sequencing data, NGS data analysis, NGS data analysis workflow, data integration, Jupyter notebook, CWL format, bio.tools |
is listed by: bio.tools is listed by: Debian |
Intramural Research Program of the National Library of Medicine NIH | DOI:10.7490/f1000research.1117155.1 | Free, Freely available | biotools:pm4ngs | https://bio.tools/pm4ngs | SCR_019164 | SciCrunch Registry | Project Manager for Next Generation Sequencing | 2026-10-10 12:41:57 | 1 | |||||
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Panaroo Resource Report Resource Website 10+ mentions |
Panaroo (RRID:SCR_021090) | data analysis software, data processing software, software application, software resource | Software pipeline for pangenome investigation. Shares information between genomes to correct errors. Can call large structural variants.Fast and scalable to over 10k bacterial genomes. | pangenome investigation, correct errors, genomes, large structural variants, bacterial genomes | Free, Available for download, Freely available | https://gtonkinhill.github.io/panaroo/#/gettingstarted/quickstart | SCR_021090 | SciCrunch Registry | Bacterial Pangenome Analysis Pipeline | 2026-10-10 12:42:22 | 32 | |||||||||
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Creative Peptides: Formulation Development Service Resource Resource Report Resource Website |
Creative Peptides: Formulation Development Service Resource (RRID:SCR_022223) | instrument resource | Service to determine optimal dosage form, composition and manufacturing route for pharmaceutical products. | Creative Peptides, biomedical resource, optimal dosage form, pharmaceutical products | has parent organization: Creative Peptides | Restricted | SCR_022223 | SciCrunch Registry | Formulation Development | 2026-10-10 12:41:55 | 0 | |||||||||
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Creative Peptides: Peptide Lead Optimization Service Resource Resource Report Resource Website |
Creative Peptides: Peptide Lead Optimization Service Resource (RRID:SCR_022222) | instrument resource | Provides optimized one stop solution for peptide lead drugs. Used to improve upon lead molecule that demonstrates activity at target of interest by optimizing its potency or selectivity at target and its absorption, distribution, metabolism and elimination properties. | Creative Peptides, biomedical service, peptide lead drugs, lead molecule improvement, optimizing potency, optimizing selectivity at target | has parent organization: Creative Peptides | Restricted | SCR_022222 | SciCrunch Registry | Peptide Lead Optimization | 2026-10-10 12:41:59 | 0 | |||||||||
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Creative Peptides Peptide Drug Bioconjugations Service Resource Resource Report Resource Website |
Creative Peptides Peptide Drug Bioconjugations Service Resource (RRID:SCR_022221) | service resource | Custom peptide synthesis, modification, and conjugation services involve chemical modification of peptide at highly specific sites. This allows for attachment of drugs or bioactive molecules though variety of coupling techniques. | Creative Peptides, conjugation services, peptide, drugs or bioactive molecules attachment, biomedical service | has parent organization: Creative Peptides | Restricted | SCR_022221 | SciCrunch Registry | Peptide Drug Bioconjugations | 2026-10-10 12:41:52 | 0 | |||||||||
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Tandem Repeats Finder Resource Report Resource Website 100+ mentions |
Tandem Repeats Finder (RRID:SCR_022065) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to locate and display tandem repeats in DNA sequences. Used to analyze DNA sequences. | locate and display tandem repeats, analyze DNA sequences, tandem repeat, DNA sequence | PMID:9862982 | Free, Available for download, Freely available | SCR_022065 | SciCrunch Registry | 2026-10-10 12:41:55 | 443 | ||||||||||
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Brain Cell Methylation Viewer Resource Report Resource Website 1+ mentions |
Brain Cell Methylation Viewer (RRID:SCR_020954) | mC Viewer | analysis service resource, data access protocol, data or information resource, production service resource, service resource, software resource, web service | Viewer for DNA Methylation Atlas of Mouse Brain at Single Cell Resolution. Browser to interactively explore single cell methylome dataset including exploration of methylation diversity of one gene at single-cell or cell-type level, exploration of cell type composition of adult mouse brain dissection regions and anatomical structures, explorartion of spatial distribution and methylation signature genes of one cell type. | BRAIN Initiative Cell Census Network, mouse brain, cell types, epigenomes, single cell exploration, methylome dataset | has parent organization: Salk Institute for Biological Studies | DOI:10.1101/2020.04.30.069377 | Free, Freely available | SCR_020954 | SciCrunch Registry | Neomorph: Brain Cell Methylation Viewer | 2026-10-10 12:42:22 | 2 | |||||||
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Creative Peptides Total Peptide Library Construction Service Resource Resource Report Resource Website |
Creative Peptides Total Peptide Library Construction Service Resource (RRID:SCR_022219) | service resource | Service uses bioinformatics methods to compress peptide information, which can integrate information of multiple peptide into one peptide. Provides collection of small peptide of specific length and different sequences, which includes permutation and combination of various amino acid sequences in short peptide of this length.Total peptide library for new drug research and development. | Creative Peptides, biomedical service, peptide information, amino acid sequences, short peptide, peptide library | has parent organization: Creative Peptides | Restricted | SCR_022219 | SciCrunch Registry | Total Peptide Library Construction Technology | 2026-10-10 12:42:23 | 0 | |||||||||
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Waters: SQD2 LC/MS system Resource Report Resource Website 10+ mentions |
Waters: SQD2 LC/MS system (RRID:SCR_022217) | instrument resource | System includes SQD2 as single quadrupole MS with Waters H-Class Acquity UPLC, operated as open access platform for trained users. SQ Detector2 is single quadrupole mass detector for chromatography compatible with range of chromatography platforms and ionization sources. | SQ Detector2, instrument, equipment, USEDit, single quadrupole MS, mass spectrometer, liquid chromatography, Waters H-Class Acquity UPLC, chromatography platform, chromatography quadrupole mass detector |
uses: Waters SQ Detector 2 Mass Spectrometer is used by: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility |
SCR_022217 | SciCrunch Registry | Stanford Waters SQD2 LC/MS system | 2026-10-10 12:41:59 | 12 | ||||||||||
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CSpritz Resource Report Resource Website 1+ mentions |
CSpritz (RRID:SCR_021884) | data access protocol, software resource, web service | Web tool for prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs. | Intrinsic protein disorder segments prediction, homology, secondary structure, linear motifs, annotation | Italian Ministry of Education ; University of Padova |
DOI:10.1093/nar/gkr411 | Free, Freely available | SCR_021884 | SciCrunch Registry | 2026-10-10 12:42:23 | 2 | |||||||||
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SIGNOR Resource Report Resource Website 50+ mentions |
SIGNOR (RRID:SCR_018485) | data or information resource, data repository, database, service resource, storage service resource | Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles. | Signal transduction data, signaling information, published data collection, activity flow, chemical inhibitor, human proteome, manually annotated data, protein, protein relationship, FAIR data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: REDIportal |
ELIXIR-IIB ; EMBL-EBI ; Italian Association for Cancer Research ; Italian Node of the European ELIXIR infrastructure |
PMID:31665520 | Free, Available for download, Freely available | biotools:signor | https://bio.tools/signor | SCR_018485 | SciCrunch Registry | SIGnaling Network Open Resource, SIGNOR 2.0 | 2026-10-10 12:41:54 | 61 | |||||
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LabSolutions Resource Report Resource Website 50+ mentions |
LabSolutions (RRID:SCR_018241) | data analysis software, data processing software, software application, software resource | Software package for data analysis by Shimadzu Oceania. | Data analysis system, data analysis, Shimadzu Oceania | Restricted | SCR_018241 | SciCrunch Registry | LabSolutions Software | 2026-10-10 12:41:50 | 87 | ||||||||||
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Institute for Advanced Biosciences Resource Report Resource Website 1+ mentions |
Institute for Advanced Biosciences (RRID:SCR_008526) | data or information resource, database, organization portal, portal | The Institute for Advanced Biosciences, Keio University, is an academic research institute pioneering the new life science field of Systems Biology, using both experimental and computational biology. There are several groups working in collaboration, focusing mainly on genome biology and engineering, genome design and synthetic biology, metabolic engineering, proteomics, metabolomics, RNA biology, bioinformatics and computational biology. Using cutting-edge technologies, intracellular components can be analyzed comprehensively to construct computer simulation models that can find numerous applications in fields such as biomedical, environmental, and agricultural science. Experimental and computational facilities are located in Tsuruoka, Yamagata prefecture, in northern Japan while the SFC campus, in the Tokyo area, hosts the bioinformatics laboratory and most undergraduate curricular activities. IAB has successfully attracted very significant funding for multiple research projects from major funding organizations including the New Energy and Industrial Technology Development Organization (NEDO) (2002-2006), for bioprocesses and cell modeling, the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and its COE network, for biosimulation and systems biology (2003-2008), the Japan Science and Technology Agency (CREST, 2004-2009) for simulation and systems biology, the Ministry of Health, for cancer biology (2005), as well as from Yamagata prefecture and Tsuruoka city, 2001-2006 and 2006-2011). Over the past few years, IAB scientists have accumulated several awards including the 1st prize during the 5th Japan Biotechnology Business Competition (2005), the Minister of State for Science and Technology Policy award in recognition for industry-academia-government collaboration performance (2004), the IBM Shared University Research Award (2003), and the Nihon Kogyo Shimbunsha Award (2003) during the 17th Leading-edge Technology for Originality and Creativity. Sponsor. This study was supported by a grant from the Global COE Program entitled, Human Metabolomic Systems Biology and by a Grant-in-Aid for Scientific Research on Priority Areas Systems Genomes and on Lifesurveyor from the Ministry of Education, Culture, Sports, Science and Technology of Japan as well as research funds from the Yamagata prefectural government and the City of Tsuruoka. | nif-0000-30595 | http://www.ogic.ca/projects/g2d_2/ | SCR_008526 | SciCrunch Registry | IAB | 2026-10-10 12:42:32 | 7 | ||||||||||
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Functional Analysis of Diffusion Tensor Resource Report Resource Website 1+ mentions |
Functional Analysis of Diffusion Tensor (RRID:SCR_008888) | FADTTS | data processing software, software application, software resource | Pipeline developed for delineating the association between multiple diffusion properties along major white matter fiber bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these white matter tract properties in various diffusion tensor imaging studies. FADTTS can be used to facilitate understanding of normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. The advantages of FADTTS compared with the other existing approaches are that they are capable of modelling the structured inter-subject variability, testing the joint effects, and constructing their simultaneous confidence bands. | genomic analysis, diffusion tensor imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Spatial Statistical Parametric Mapping |
Academic Free License | nlx_151351 | SCR_008888 | SciCrunch Registry | Functional Analysis of Diffusion Tensor Tract Statistics | 2026-10-10 12:43:31 | 3 | |||||||
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LAPSTRUCT Resource Report Resource Website 1+ mentions |
LAPSTRUCT (RRID:SCR_007550) | software application, software resource | Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | Free | nlx_154589, SCR_009367, nlx_154209 | SCR_007550 | SciCrunch Registry | R/LAPSTRUCT, LAPlacian eigenfunctions learn population STRUCTure | 2026-10-10 12:42:31 | 3 | ||||||||
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Division of Aquaculture Resource Report Resource Website 1+ mentions |
Division of Aquaculture (RRID:SCR_008484) | data or information resource, organization portal, portal | This web site is your introduction to the world of Florida Aquaculture. It represents a compilation of information about a division in the Florida Department of Agriculture and Consumer Services-the Division of Aquaculture. The Division plays a key role in the regulation of aquaculture facilities and shellfish processing plants, is responsible for opening/closing of shellfish harvesting waters to protect human health, ensures the continued productivity of oyster reefs through a restoration program and issues leases of submerged state lands for aquaculture. The creation of this division is unprecedented for a state agriculture department. Florida''s Division of Aquaculture is one-of-a-kind and serves a unique industry like no other in the United States. Please browse this site and learn more about Florida Aquaculture. I welcome your comments on the topics contained in this web site. | nif-0000-30458 | SCR_008484 | SciCrunch Registry | Division of Aquaculture | 2026-10-10 12:42:32 | 1 |
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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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