Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
EvidenceFinder Resource Report Resource Website 1+ mentions |
EvidenceFinder (RRID:SCR_013764) | software resource, web application | A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched. | web application, software resource, literature search, bio.tools |
is used by: Europe PubMed Central is listed by: Connected Researchers is listed by: Debian is listed by: bio.tools is related to: Connected Researchers is related to: Europe PubMed Central has parent organization: Europe PubMed Central |
Wellcome Trust 098231 | DOI:10.1093/nar/gku1061 | Free, Public | biotools:evidence_finder | https://bio.tools/evidence_finder | SCR_013764 | 2026-02-12 09:46:11 | 3 | ||||||
|
YaHS Resource Report Resource Website 100+ mentions |
YaHS (RRID:SCR_022965) | software resource, software application, data analysis software, data processing software | Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies. | construction of chromosome scale scaffolds, Hi-C data, Omni-C data, scaffold contig level assemblies, chromosome scale scaffolded assemblies | Wellcome Trust | DOI:10.1101/2022.06.09.495093 | Free, Available for download, Freely available | SCR_022965 | 2026-02-12 09:47:48 | 450 | |||||||||
|
TIGER Data Portal Resource Report Resource Website 10+ mentions |
TIGER Data Portal (RRID:SCR_023626) | data or information resource, portal, disease-related portal, topical portal | Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets. | Type 2 Diabetes, genetic and epigenetic, functional data, molecular data, clinical data, pancreatic beta cells. | is related to: T2DSystems | Type 2 Diabetes | European Union Horizon 2020 ; Spanish government ; Swiss State Secretariat for Education‚ Research and Innovation ; American Diabetes Association Innovative and Clinical Translational Award ; Research England ; Wellcome Trust ; NIDDK U01 DK105535; NIDDK U01 DK085545 |
PMID:34644572 | SCR_023626 | Translational Human Pancreatic Islet Genotype Tissue-Expression Resource | 2026-02-12 09:47:41 | 18 | |||||||
|
xiNET Resource Report Resource Website 10+ mentions |
xiNET (RRID:SCR_021010) | software resource, data access protocol, web service, software application, data processing software, data visualization software | Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains. | Crosslinking mass spectrometry data visualization, linkage sites, linked peptides, crosslinking reaction product display, crosslink network maps, maps with residue resolution | Wellcome Trust | PMID:25648531 | Free, Available for download, Freely available | http://github.com/colin-combe/crosslink-viewer | SCR_021010 | Crosslink Network Maps With Residue Resolution | 2026-02-12 09:47:09 | 19 | |||||||
|
EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | data access protocol, software resource, web service, database, data or information resource | Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. | Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Warwick; Coventry; United Kingdom |
Biotechnology and Biological Sciences Research Council ; Wellcome Trust |
Restricted | biotools:Enterobase | https://bio.tools/EnteroBase | SCR_019019 | 2026-02-12 09:47:38 | 233 | |||||||
|
SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | software resource, software application, data analysis software, data processing software | Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree. | Direct coupling analysis, aligned categorical datasets, analysis, genome, bacteria, phylogenetic signal, correction, phylogenetic tree, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
COIN Center of Excellence ; Academy of Finland ; Wellcome Trust ; European Research Council |
PMID:31361894 | Free, Available for download, Freely available | biotools:SpydrPick | https://anaconda.org/bioconda/spydrpick https://bio.tools/SpydrPick |
SCR_018176 | 2026-02-12 09:47:25 | 2 | ||||||
|
SuperDCA Resource Report Resource Website 1+ mentions |
SuperDCA (RRID:SCR_018175) | software resource, software application, data analysis software, data processing software | Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis. | Protein, sequence, alignment, analysis, genome, loci, epistasis | Academy of Finland ; Wellcome Trust ; Royal Society ; European Research Council |
PMID:29813016 | Free, Available for download, Freely available | SCR_018175 | Super Direct Coupling Analysis | 2026-02-12 09:47:00 | 1 | ||||||||
|
genomics resource for animal lectins Resource Report Resource Website 1+ mentions |
genomics resource for animal lectins (RRID:SCR_018122) | data or information resource, portal, topical portal | Resource presents information about animal lectins involved in various sugar recognition processes. | Genomic, animal lectin, sugar recognition process | has parent organization: Imperial College London; London; United Kingdom | BBSRC ; Wellcome Trust ; Consortium for Functional Glycomics |
Free, Freely available | SCR_018122 | 2026-02-12 09:46:45 | 3 | |||||||||
|
HipSci Resource Report Resource Website 100+ mentions |
HipSci (RRID:SCR_003909) | HipSci | material resource, biomaterial supply resource | A UK national induced pluripotent stem (iPS) cell resource that will create and characterize more than 1000 human iPSCs from healthy and diseased tissue for use in cellular genetic studies. Between 2013 and 2016 they aim to generate iPS cells from over 500 healthy individuals and 500 individuals with genetic disease. They will then use these cells to discover how genomic variation impacts on cellular phenotype and identify new disease mechanisms. Strong links with NHS investigators will ensure that studies on the disease-associated cell lines will be linked to extensive clinical information. Further key features of the project are an open access model of data sharing; engagement of the wider clinical genetics community in selecting patient samples; and provision of dedicated laboratory space for collaborative cell phenotyping and differentiation. | stem cell, genomic variation, cellular phenotype, disease mechanism, phenotype, disease, clinical data, clinical, genetics, male, female, cell line, induced pluripotent stem cell |
is listed by: One Mind Biospecimen Bank Listing has parent organization: European Bioinformatics Institute |
Healthy, Genetic disease | Wellcome Trust ; MRC |
Acknowledgement required, Free, Public | nlx_158252 | SCR_003909 | Human Induced Pluripotent Stem Cells Initiative | 2026-02-12 09:43:43 | 115 | |||||
|
Sanger Mouse Resources Portal Resource Report Resource Website 50+ mentions |
Sanger Mouse Resources Portal (RRID:SCR_006239) | Sanger Mouse Portal, WTSI Mouse Resources Portal, WTSI Mouse Resource Portal | material resource, biomaterial supply resource | Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. | bacterial artificial chromosome, vector, embryonic stem cell, mutant mouse line, phenotype, gene, knockout, gene expression, genetics, chromosome, mutant, mouse line, mammal, marker symbol |
is listed by: One Mind Biospecimen Bank Listing is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 079643; Wellcome Trust 098051; NHGRI UO1-HG004080; NCRR 1-U42RR033192; European Union LSHG-CT-2006-037188; European Union 227490; European Union 312325; European Union 261492 |
For the scientific community | nlx_151819 | SCR_006239 | Mouse Resources Portal, Wellcome Trust Sanger Institute Mouse Resources Portal | 2026-02-12 09:44:20 | 51 | ||||||
|
Tract Based Spatial Statistics Resource Report Resource Website 1+ mentions |
Tract Based Spatial Statistics (RRID:SCR_024932) | TBSS | software application, data processing software, software resource, image analysis software | Software tool to improve sensitivity, objectivity and interpretability of analysis of multi-subject diffusion imaging studies. | analysis of multi-subject diffusion imaging studies, imaging analysis, imaging, | is a plug in for: FSL | EPSRC ; BBSRC ; MRC ; Wellcome Trust ; Multiple Sclerosis Society |
PMID:16624579 | Free, Freely available | SCR_024932 | , Tract-Based Spatial Statistics, TBSS:Tract-Based Spatial Statistics | 2026-02-12 09:48:21 | 4 | ||||||
|
XTRACT Resource Report Resource Website 1+ mentions |
XTRACT (RRID:SCR_024933) | software application, software resource | Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain. | automated tractography, tractography, human, macaque, brain | is a plug in for: FSL | Medical Research Council PhD Studentship UK ; Marie Skłodowska-Curie Individual Fellowship Grant ; Biotechnology and Biological Sciences Research Council ; Netherlands Organization for Scientific Research NWO Netherlands ; Sir Henry Dale Wellcome Trust Fellowship UK ; MRC Career Development Fellowship UK ; Wellcome Trust Collaborative Award UK ; UK Engineering and Physical Sciences Research Council ; Wellcome Trust grant UK ; Human Connectome Project ; NIMH 1U54MH091657; McDonnell Center for Systems Neuroscience at Washington University ; NIH ; UK Biobank Resource ; Wellcome Trust |
PMID:32407993 | Free, Freely available | SCR_024933 | 2026-02-12 09:48:08 | 2 | ||||||||
|
ezBIDS Resource Report Resource Website |
ezBIDS (RRID:SCR_025563) | software resource, web application | Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms. | Guided standardization, neuroimaging data, Brain Imaging Data Structure, BIDS conversion tool, convert neuroimaging data, associated metadata, interoperable, BIDS standard, | NINDS UM1NS132207; BRAIN CONNECTS ; NIBIB R01EB029272; NIBIB R01EB030896; NSF ; Kavli Foundation ; Wellcome Trust ; NIMH R01MH133701; Spanish Government |
PMID:38332144 | Free, Freely available | https://brainlife.io/ezbids/ |
SCR_025563 | ez Brain Imaging Data Structure | 2026-02-12 09:48:25 | 0 | |||||||
|
ISOLDE Resource Report Resource Website 1+ mentions |
ISOLDE (RRID:SCR_025577) | software application, software resource | Software environment to ease task of building macromolecular models into low to medium resolution experimental maps. Physically realistic environment for model building into low-resolution electron-density maps. Can generate maps directly from crystallographic F/sigF data in MTZ format and automatically re-calculate them when model changes, and/or generate "static" maps from pre-calculated F/phi data. | software environment, model building, building macromolecular models, low resolution electron density maps, experimental maps, | is a plug in for: UCSF ChimeraX | Wellcome Trust | PMID:29872003 | Free, Freely available | SCR_025577 | 2026-02-12 09:48:25 | 8 | ||||||||
|
University College London Darwin Research Core Facility Resource Report Resource Website |
University College London Darwin Research Core Facility (RRID:SCR_026345) | service resource, access service resource, core facility | Facility provides diverse range of equipment, expertise and training in field of biochemistry, molecular, structural and cellular biology. Facility consists of several research laboratories and support areas. | ABRF, biochemistry, molecular, structural and cellular biology, service, |
is listed by: ABRF CoreMarketplace has parent organization: University College London; London; United Kingdom |
Wellcome Trust ; HEFCE ; University College London |
ABRF_3028 | https://coremarketplace.org/?FacilityID=3028&citation=1 | SCR_026345 | , UCL Darwin Research Facility, Darwin Research Facility, University College London Darwin Research Facility | 2026-02-12 09:49:05 | 0 | |||||||
|
Alien-hunter Resource Report Resource Website 1+ mentions |
Alien-hunter (RRID:SCR_015967) | standalone software, software application, software resource | Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer. | Horizontal Gene Transfer, Interpolated Variable Order Motifs, gene, transfer, interpolated, variable, motif, prediction, hgt, ivom |
is listed by: Debian is listed by: OMICtools works with: Artemis: Genome Browser and Annotation Tool |
Wellcome Trust | PMID:16837528 DOI:10.1093/bioinformatics/btl369 |
Free, Available for download | OMICS_08280 | https://sources.debian.org/src/alien-hunter/ https://sources.debian.org/src/alien-hunter/ |
SCR_015967 | 2026-02-12 09:46:40 | 5 | ||||||
|
FLIMfit Resource Report Resource Website 1+ mentions |
FLIMfit (RRID:SCR_016298) | software toolkit, software application, software resource | Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | fluorescence, lifetime, imaging, microscopy, dataset, global, analysis, multiwell, plate, routine | United Kingdom Biotechnology and Biological Sciences Research Council BBSRC BB/E003621/1; United Kingdom Technology Strategy Board Technology Award CHBT/007/00030; Wellcome Trust WT 095931/Z/11/Z |
PMID:23940626 DOI:10.1371/journal.pone.0070687 |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/flimfit/FLIMfit | SCR_016298 | 2026-02-12 09:46:28 | 3 | ||||||||
|
VGNC Resource Report Resource Website 10+ mentions |
VGNC (RRID:SCR_017514) | data or information resource, database, service resource | 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. | Vertebrate, gene, nomenclature, data, symbol | is related to: HGNC | NHGRI U24 HG003345; Wellcome Trust |
Free, Freely available | SCR_017514 | Vertebrate Gene Nomenclature Committee | 2026-02-12 09:46:35 | 13 | ||||||||
|
Metabolic Subphenotype Predictor Resource Report Resource Website 1+ mentions |
Metabolic Subphenotype Predictor (RRID:SCR_027192) | source code, software resource | Software repository contains code for Inference of T2D metabolic subphenotypes (MuscleIR, Beta-cell Function, Incretin Effect, Hepatic IR), Identification of dominant metabolic subphenotype, Feature extraction from glucose tiemseries, Extraction of reduced representation of glucose tiemseries,Visualization of metabolic phenotypes based on various glucose-related metrics,Concordance between CGM and Venous glucose values from at home and at clinical setting, Classification of metabolic subphenotypes. | Inference of T2D metabolic subphenotypes, identification of dominant metabolic subphenotype, extraction from glucose tiemseries, visualization of metabolic phenotypes, classification of metabolic subphenotype, s | NIDDK R01 DK110186; Stanford PHIND award ; Stanford Diabetes Research Center ; Wellcome Trust ; NIDDK U01 DK105535; NIDDK U01 DK085545; NIDDK UM1DK126185; NHLBI 2T32HL09804911 |
PMID:39715896 | Free, Available for download, Freely available | SCR_027192 | 2026-02-12 09:49:10 | 1 | |||||||||
|
Souporcell Resource Report Resource Website 1+ mentions |
Souporcell (RRID:SCR_027462) | source code, software application, software resource | Software tool to cluster cells using the genetic variants detected within the scRNAseq reads. Robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Used for clustering scRNAseq by genotypes. | Clustering scRNAseq by genotypes, cluster cells, genetic variants, scRNAseq reads, | Wellcome Trust ; UK Medical Research Council ; British Heart Foundation |
PMID:32366989 | Free, Available for download, Freely available | SCR_027462 | 2026-02-12 09:48:37 | 1 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
