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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
PAFScaff Resource Report Resource Website 1+ mentions |
PAFScaff (RRID:SCR_017976) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software as Pairwise mApping Format reference based Scaffold anchoring and super scaffolding tool. Dsigned for mapping genome assembly scaffolds to closely related chromosome level reference genome assembly. | Pairwise, mapping, reference, scaffold, genomics, scaffolding, assembly, genome, chromosome, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:PAFScaff | https://github.com/slimsuite/pafscaff/blob/master/PAFScaff.md, https://slimsuite.github.io/pafscaff/, https://bio.tools/PAFScaff | SCR_017976 | Pairwise mApping Format reference-based Scaffold | 2026-09-19 12:53:44 | 4 | |||||||
|
CandiMeth Resource Report Resource Website 1+ mentions |
CandiMeth (RRID:SCR_017974) | CandiMeth | analysis service resource, data analysis software, data processing software, production service resource, service resource, software application, software resource | Software tool for visualisation and quantification of DNA methylation at candidate features. | DNA, methylation, candidate feature, visualisation, quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy |
ESRC/BBSRC ; Medical Research Council |
Free, Freely available | biotools:CandiMeth | http://bit.do/candimeth, https://usegalaxy.org/u/sarajayne-thursby/w/candimeth-8, https://bio.tools/CandiMeth | SCR_017974 | CANDIdate feature METHylation | 2026-09-19 12:53:44 | 2 | |||||
|
Select Science: Carestream Gel Logic 212 PRO Imaging System Resource Report Resource Website 10+ mentions |
Select Science: Carestream Gel Logic 212 PRO Imaging System (RRID:SCR_018029) | instrument resource | Automated gel imaging system for imaging fluorescence or colorimetric data in sample formats such as gels (DNA/Coomassie/Silver stain) membranes, and 96 well plates. Features include autofocusing and directed autoexposure. | imager, Bruker BioSpin, imaging, fluorescence, colorimetric, gel, data, instrument, equipment | is listed by: USEDit | SCR_018601 | SCR_018029 | Carestream Gel Logic 212 PRO Imaging System, Gel Logic 212 PRO, Bruker BioSpin Gel Logic 212 PRO, Carestream Gel Pro 212 Imager | 2026-09-19 12:53:45 | 43 | |||||||||
|
VEnCode Resource Report Resource Website 1+ mentions |
VEnCode (RRID:SCR_018024) | VEnCode | data analysis software, data processing software, software application, software resource | Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases. | FANTOM5 consortium, data, CAGE enhancer, transcription site database, intersectional genetics, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/552984 | Free, Available for download, Freely available | BioTools:VEnCode, biotools:VEnCode | https://bio.tools/VEnCode, https://bio.tools/VEnCode, https://bio.tools/VEnCode | SCR_018024 | Versatile Entry Codes | 2026-09-19 12:53:45 | 1 | |||||
|
sietraj Resource Report Resource Website 1+ mentions |
sietraj (RRID:SCR_018021) | simulation software, software application, software resource | Software tool for binding free energies from Amber-generated MD trajectories. Alternative to MM-PBSA software provided by AMBER distribution. Virtual alanine mutations are also possible. Solvated interaction energies are calculated using parameters that have been fitted to reproduce binding free energies of data set of 99 protein-ligand complexes. | Binding free energy, Amber, MD trajctory, MM-PBSA, virtual alanine mutation, solvated interaction energy, calculation, parameter, protein-ligand complex | Restricted | SCR_018021 | 2026-09-19 12:53:45 | 2 | |||||||||||
|
Worm Lab Resource Report Resource Website 1+ mentions |
Worm Lab (RRID:SCR_017669) | data analysis software, data processing software, software application, software resource | Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays. | MBF Bioscience, imaging, tracking, analysis, C.elegans, nematode, collect, data, worm, omega, bend, coiling, reversal, entanglement, locomotry, behavior, crawling, swimming, assay | Restricted | SCR_017669 | 2026-09-19 12:53:44 | 8 | |||||||||||
|
MOON Resource Report Resource Website 1+ mentions |
MOON (RRID:SCR_018005) | data analysis software, data processing software, software application, software resource, software toolkit | Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid. | Diagnosis, rare disease, next generation sequencing, NGS, data, artificial intelligence, analysis, Diploid | Restricted | SCR_018005 | 2026-09-19 12:53:45 | 6 | |||||||||||
|
Vesselucida Explorer Resource Report Resource Website 1+ mentions |
Vesselucida Explorer (RRID:SCR_017674) | data analysis software, data processing software, software application, software resource | Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more. | MBF Bioscience, analysis, vasculature, specific, metric, segment, node, count, frequency, anastomoses, vessel, surface, volume | works with: Vesselucida 360 | Restricted | SCR_017674 | 2026-09-19 12:53:44 | 2 | ||||||||||
|
cytoHubba Resource Report Resource Website 100+ mentions |
cytoHubba (RRID:SCR_017677) | data analysis software, data processing software, network analysis software, software application, software resource | Software tool for identifying hub objects and sub-networks from complex interactome. Predicts and explore nodes and subnetworks in given network by several topological algorithms. Provides interface to analyze topology of protein-protein interaction networks, such as human, yeast, rat, mouse, fly etc. Plugin works with Cytoscape 2.6 or above, which requires Java 1.5 or above. | Identify, network, subnetwork, topological, algorithm, analyze, protein, interaction, hub, object, intercome | is a plug in for: Cytoscape | Ministry of Science and Technology (MOST) ; Taiwan |
PMID:25521941 | Free, Available for download, Freely available | http://hub.iis.sinica.edu.tw/cytoHubba/ | SCR_017677 | cytoHubba 1.6 | 2026-09-19 12:53:44 | 451 | ||||||
|
Digimeter: DS5 Isolated Bipolar Current Stimulator Resource Report Resource Website 1+ mentions |
Digimeter: DS5 Isolated Bipolar Current Stimulator (RRID:SCR_018001) | instrument resource | Stimulator allows computer control of stimulus amplitude and timing parameters. Designed to speed up and enhance human peripheral nerve diagnostics by facilitating semi-automated nerve excitability tests. It also has roles in wider aspects of clinical neurophysiology research, including psychological, vestibular system and nociceptive testing. CE marked medical device under European Medical Device Regulation. | Medical, device, stimulator, computer control, timing parameter, human peripheral nerve, diagnostic, excitability test, clinical neurophysiology | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018001.pdf | https://www.digitimer.com/wp-content/uploads/2019/09/ds5.pdf | SCR_018001 | 2026-09-19 12:53:45 | 1 | ||||||||||
|
fineSTRUCTURE Resource Report Resource Website 10+ mentions |
fineSTRUCTURE (RRID:SCR_018170) | data analysis software, data processing software, software application, software resource | Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data. | Identifying population structure, dense sequencing data, Bayesian clustering, large dataset, data, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:finestructure | https://bio.tools/finestructure | SCR_018170 | FineSTRUCTURE version 2 | 2026-09-19 12:53:48 | 23 | |||||||
|
SAVES Resource Report Resource Website 100+ mentions |
SAVES (RRID:SCR_018219) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for structure validation in homology modeling. Used to validate of obtained crude models. Structure analysis and validation server. | Structure validation, homology modeling, obtained model, analysis, validation server | has parent organization: University of California at Los Angeles; California; USA | Free, Freely available | SCR_018219 | SAVES v5.0, Structure Analysis and Verification Server | 2026-09-19 12:53:48 | 219 | |||||||||
|
Umap Resource Report Resource Website 100+ mentions |
Umap (RRID:SCR_018217) | UMAP | data processing software, data visualization software, software application, software resource, software toolkit | Software package as dimension reduction technique that can be used for visualization similar to t-SNE, but also for general non-linear dimension reduction. Used for dimensionality reduction for visualizing single-cell data. | Dimension reduction technique, data visualization, singel cell data | is listed by: Debian | Free, Available for download, Freely available | https://github.com/lmcinnes/umap, https://sources.debian.org/src/umap-learn/ | SCR_018217 | Uniform Manifold Approximation and Projection | 2026-09-19 12:53:48 | 179 | |||||||
|
ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling. | Chromatin loop, CHi-C promoter, data, Hi-C visualization, interaction calling, data, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31118054 | Free, Freely available | biotools:ChiCMaxima | https://bio.tools/ChiCMaxima | SCR_018178 | 2026-09-19 12:53:48 | 2 | |||||||
|
SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | software resource, web application | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Key Research and Development Program of China 2016YFD0100801; National Key Research and Development Program of China 2018YFD0100803; National Natural Science Foundation of China 31701415 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/, https://bio.tools/SnpHub | SCR_018177 | 2026-09-19 12:53:48 | 1 | |||||||
|
Bustools Resource Report Resource Website 10+ mentions |
Bustools (RRID:SCR_018210) | data analysis software, data processing software, software application, software resource | Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. | Single cell RNAseq workflow, single cell RNAseq dataset, error correct barcode, collapse UMI, produce gene count, produce transcript compatibility count matrice |
is listed by: Debian is listed by: OMICtools works with: kb_python |
DOI:10.1101/673285 | Free, Available for download, Freely available | OMICS_33004 | https://sources.debian.org/src/bustools/ | SCR_018210 | 2026-09-19 12:53:48 | 19 | |||||||
|
SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | data analysis software, data processing software, software application, software resource | 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 ; European Research Council ; Wellcome Trust |
PMID:31361894 | Free, Available for download, Freely available | biotools:SpydrPick | https://anaconda.org/bioconda/spydrpick, https://bio.tools/SpydrPick | SCR_018176 | 2026-09-19 12:53:48 | 3 | ||||||
|
SuperDCA Resource Report Resource Website 1+ mentions |
SuperDCA (RRID:SCR_018175) | data analysis software, data processing software, software application, software resource | 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 ; European Research Council ; Royal Society ; Wellcome Trust |
PMID:29813016 | Free, Available for download, Freely available | SCR_018175 | Super Direct Coupling Analysis | 2026-09-19 12:53:48 | 1 | ||||||||
|
How many cells Resource Report Resource Website 10+ mentions |
How many cells (RRID:SCR_018184) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for calculating number of cells that must be sampled in order to see at least n cells of each type for single cell genomics experiments. | Calculating cell number, single cell genomic, genomic experiment, cell type number, New York Genome Center, Satija Lab | Free, Freely available | SCR_018184 | Satija Lab: How Many Cells | 2026-09-19 12:53:48 | 22 | ||||||||||
|
Blackfynn Discover Resource Report Resource Website 1+ mentions |
Blackfynn Discover (RRID:SCR_018068) | data or information resource, data repository, data set, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. Data repository for scientific data. Open data library to explore neuroscience data for neurodegenerative diseases for which there are no disease modifying treatments. | Neuroscience data, data repository, neurogenerative disease |
is used by: SPARC Portal is related to: Pennsieve Data Management Platform is organization facet of: SPARC Portal |
epilepsy, Parkinson, Alzheimer, neurodegenerative disease | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_018068 | 2026-09-19 12:53:46 | 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.
