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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.
https://git.integromics.fr/published/predomics
Software package for metagenomics data. Discovers accurate predictive signatures and provides unprecedented interpretability. Package contains three methods for suppervised learning based on ternary coefficients. Used to discover classification models for quantitative metagenomics data.
Proper citation: Predomics (RRID:SCR_017415) Copy
https://jcr.clarivate.com/JCRLandingPageAction.action
Web tool with systematic, objective means to critically evaluate journals, with quantifiable, statistical information based on citation data. Provides information about academic journals in natural sciences and social sciences, including impact factors in database integrated with Web of Science. Sourced from Web of Science Core Collection,citation index on Web of Science platform.
Proper citation: Journal Citation Reports (RRID:SCR_017656) Copy
http://biocc.hrbmu.edu.cn/CellMarker/
Database provides cell markers for various cell types in tissues of human and mouse. Manually curated resource of cell markers in human and mouse. Provides user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Summarized marker prevalence in each cell type is graphically presented., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CellMarker (RRID:SCR_018503) Copy
http://www.mirtoolsgallery.org/miRToolsGallery/node/1055
Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: miRanda (RRID:SCR_017496) Copy
Generates, characterises and collects cell lines which are of interest for veterinary research and diagnostics. Collection includes cell lines of farm animals such as cattle, pig, horse, sheep, goat and poultry and other mammals, birds, reptiles, fishes and insects (70 species).Authentication and quality-control tests (tests for contamination with mycoplasms, bacteria, BVDV) of the cultures are done routinely.Cell cultures are provided to scientists of the Friedrich-Loeffler-Institute and other non-commercial institutions worldwide after consultation of a scientific staff member of the CCLV.
Proper citation: Collection of Cell Lines in Veterinary Medicine (RRID:SCR_023182) Copy
http://www.people.fas.harvard.edu/~junliu/em/em.htm
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.
Proper citation: EM-DECODER (RRID:SCR_000023) Copy
https://github.com/wilsonGW/SomaDetection
Source code for a machine learning method to detect somas on confocal microscopic images of the Drosophila brain. The method can be applied to the original raw images where the noises are not removed and the number of somas is unknown.
Proper citation: SomaDetection (RRID:SCR_015717) Copy
http://viewer.shigen.info/cgi-bin/crispr/crispr.cgi
Web tool to show micro homology sequences striding over double strand break point created by CRISPR/Cas9 system. Used to search for CRISPR target site with micro-homology sequences. Used to predict deletion pattern.
Proper citation: NBRP Medaka CRISPR target site (RRID:SCR_018159) Copy
Database lists names of prokaryotes that have been validly published in International Journal of Systematic and Evolutionary Microbiology directly or by inclusion in Validation List, under Rules of International Code of Nomenclature of Bacteria. Has classification of prokaryotes and information on prokaryotic nomenclature and culture collections.
Proper citation: LPSN Database (RRID:SCR_018151) Copy
http://nucleobytes.com/index.php/4peaks
Software application for viewing and editing sequence trace files.
Proper citation: 4Peaks (RRID:SCR_000015) Copy
Database by Medisapiens Ltd. as fully integrated and annotated human gene expression data source. All genes are comparable across all samples. Provides data analysis options using database of human transcriptome.
Proper citation: IST Online (RRID:SCR_018794) Copy
Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.
Proper citation: CIS-BP (RRID:SCR_017236) Copy
Open online platform for single cell RNA-seq. Provides data management and analytics. Used to analyze public and private datasets and you can choose between several best practices workflows and browse existing analyses.
Proper citation: FASTGenomics (RRID:SCR_022898) Copy
https://vertebrate.genenames.org/
Software resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.
Proper citation: VGNC (RRID:SCR_017514) Copy
https://www.robotreviewer.net/
Software tool as machine learning system that automatically assesses bias in clinical trials. From PDF formatted trial report determines risks of bias for domains defined by Cochrane Risk of Bias (RoB) tool, and extracts supporting text for these judgments.
Proper citation: Robot Reviewer (RRID:SCR_018961) Copy
https://web.stanford.edu/group/dlab/optogenetics/
Database of different optogenetics resources like hardware, protocols, sequence information.
Proper citation: Optogenetics Resource Center (RRID:SCR_017513) Copy
https://www.estimationstats.com/#/
Web application for data analysis and visualizing effect sizes. Data analysis with estimation graphics.
Proper citation: Estimation Stats (RRID:SCR_018321) Copy
http://www.diabetesbiobank.org
Non-profit initiative of the Belgian Diabetes Registry (BDR), the Beta Cell Therapy consortium (BCT), the Flemish Center for Medical Innovation (CMI) and the Brussels Institute for Research and Innovation (Innoviris). It aims to support medical research into the epidemiology, prevention, diagnosis and treatment of diabetes.
Proper citation: Diabetes Biobank Brussels (RRID:SCR_015571) Copy
https://github.com/hash-bang/Reflib-Node
Reference library processing for JavaScript. Reference library processing for NodeJS.
Proper citation: RefLib (RRID:SCR_018320) Copy
https://hcup-us.ahrq.gov/nisoverview.jsp
Family of healthcare databases and related software tools and products developed through Federal-State-Industry partnership. Databases bring together data collection of State data organizations, hospital associations, private data organizations, and Federal government to create national information resource of encounter-level healthcare data. HCUP includes largest collection of longitudinal hospital care data in the United States, with all-payer, encounter-level information beginning in 1988. These databases enable research on broad range of health policy issues, including cost and quality of health services, medical practice patterns, access to healthcare programs, and outcomes of treatments at the national, State, and local market levels.
Proper citation: Healthcare Cost and Utilization Project (RRID:SCR_024410) Copy
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