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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.
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.
Proper citation: EvidenceFinder (RRID:SCR_013764) Copy
https://github.com/c-zhou/yahs
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.
Proper citation: YaHS (RRID:SCR_022965) Copy
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.
Proper citation: TIGER Data Portal (RRID:SCR_023626) Copy
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.
Proper citation: xiNET (RRID:SCR_021010) Copy
http://enterobase.warwick.ac.uk/
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.
Proper citation: EnteroBase (RRID:SCR_019019) Copy
https://github.com/santeripuranen/SpydrPick
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.
Proper citation: SpydrPick (RRID:SCR_018176) Copy
https://github.com/santeripuranen/SuperDCA
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.
Proper citation: SuperDCA (RRID:SCR_018175) Copy
http://www.imperial.ac.uk/research/animallectins
Resource presents information about animal lectins involved in various sugar recognition processes.
Proper citation: genomics resource for animal lectins (RRID:SCR_018122) Copy
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.
Proper citation: HipSci (RRID:SCR_003909) Copy
http://www.sanger.ac.uk/mouseportal/
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.
Proper citation: Sanger Mouse Resources Portal (RRID:SCR_006239) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS
Software tool to improve sensitivity, objectivity and interpretability of analysis of multi-subject diffusion imaging studies.
Proper citation: Tract Based Spatial Statistics (RRID:SCR_024932) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/XTRACT
Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.
Proper citation: XTRACT (RRID:SCR_024933) Copy
https://brainlife.io/docs/using_ezBIDS/
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.
Proper citation: ezBIDS (RRID:SCR_025563) Copy
https://tristanic.github.io/isolde/
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.
Proper citation: ISOLDE (RRID:SCR_025577) Copy
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.
Proper citation: University College London Darwin Research Core Facility (RRID:SCR_026345) Copy
http://www.sanger.ac.uk/science/tools/alien-hunter
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.
Proper citation: Alien-hunter (RRID:SCR_015967) Copy
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.
Proper citation: FLIMfit (RRID:SCR_016298) 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://github.com/aametwally/Metabolic_Subphenotype_Predictor
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.
Proper citation: Metabolic Subphenotype Predictor (RRID:SCR_027192) Copy
https://github.com/wheaton5/souporcell
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.
Proper citation: Souporcell (RRID:SCR_027462) Copy
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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.
