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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Neutron Scattering Length and Cross Sections Resource Report Resource Website 1+ mentions |
Neutron Scattering Length and Cross Sections (RRID:SCR_019140) | data or information resource, service resource | Web tool for thermal neutron cross sections. Data of scattering lengths and corresponding scattering and absorption cross sections of elements. Data go through element number 96Cm. Used for study of condensed matter structure and dynamics. | NIST Center for Neutron Research, thermal neutron cross sections, scattering lengths, condensed matter, condensed matter structure, condensed matter dynamics, absorption cross sections, scattering cross sections, data | DOI:10.1080/10448639208218770 | Free, Freely available | SCR_019140 | 2026-09-05 06:28:46 | 5 | ||||||||||
|
Neural Module Resource Report Resource Website 1+ mentions |
Neural Module (RRID:SCR_019270) | data analysis software, data processing software, software application, software resource | Neural Module by Axion BioSystems Inc, provides simplified approach to set up, execution and analysis of neural experiments. Enables Maestro Pro and Edge to record and analyze key parameters of neural network function, including activity, synchrony, and network oscillations. | Axion BioSystems Inc, neural data, neural network function, neural activity, neural synchrony, network oscillation, data analysis, neural experiment, data | Restricted | SCR_019270 | Neural Software Module, NeuralMetricTool | 2026-09-05 06:28:48 | 5 | ||||||||||
|
SoftWoRx software Resource Report Resource Website 10+ mentions |
SoftWoRx software (RRID:SCR_019157) | data acquisition software, data processing software, data visualization software, image acquisition software, image analysis software, image processing software, software application, software resource | Software for acquisition, deconvolution, processing, analysis, and display of DeltaVision images. Used in DeltaVision OMX SR imaging system., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | GE Healthcare, DeltaVision OMX SR, imaging system, image, data | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_019157 | softWoRx 7.0, softWoRx 6.5.2 | 2026-09-05 06:28:46 | 35 | ||||||||||
|
Deep Collaborative Learning Resource Report Resource Website |
Deep Collaborative Learning (RRID:SCR_019258) | DCL | data analysis software, data processing software, software application, software resource | Software tool as deep collaborative learning with application to study of multimodal brain development. Uses deep network to represent original data and then seeks their correlations, while also linking data representation with phenotypical information. | Data fusion method, nonlinear predictive relationship, functional magnetic resonance imaging, brain research, data, data correlation, phenotypical information | has parent organization: Tulane University; Louisiana; USA | Free, Available for download, Freely available | SCR_019258 | dcl_model | 2026-09-05 06:28:48 | 0 | ||||||||
|
SoupX Resource Report Resource Website 50+ mentions |
SoupX (RRID:SCR_019193) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data. | Estimation, removal, cell free mRNA contamination, droplet based, single cell RNA-seq data, RNA-seq data, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:soupx | https://bio.tools/soupx | SCR_019193 | 2026-09-05 06:28:47 | 87 | ||||||||
|
DatA Tag Suite Resource Report Resource Website |
DatA Tag Suite (RRID:SCR_019236) | DATS | data or information resource, narrative resource, software resource, software toolkit, standard specification | Software suite to enable discoverability of datasets. Enables submission of metadata on datasets to DataMed. Has core set of elements, which are generic and applicable to any type of dataset, and extended set that can accommodate more specialized data types. Platform independent model developed by NIH BD2K bioCADDIE project for DataMed Data Discovery Index prototype being developed. Also available as annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex. | Data processing, data discovery, metadata submission, DataMed, data, discovery | ELIXIR EXCELERATE ; ELIXIR-UK ; NIAID U24 AI117966 |
PMID:28585923 | Free, Freely available | SCR_019236 | 2026-09-05 06:28:47 | 0 | ||||||||
|
NSW BioNet Resource Report Resource Website 10+ mentions |
NSW BioNet (RRID:SCR_019162) | data or information resource, data repository, portal, service resource, storage service resource | Repository for biodiversity data products managed by Department of Planning, Industry and Environment, New South Wales, Australia. It stores species sightings, systematic surveys, threatened biodiversity records and species names. | Species sightings, systematic surveys, threatened biodiversity records, species names, data | Restricted | SCR_019162 | New South Wales BioNet | 2026-09-05 06:28:47 | 33 | ||||||||||
|
CloudMerge Resource Report Resource Website 1+ mentions |
CloudMerge (RRID:SCR_016051) | data compression software, data processing software, software application, software resource, source code | Software for merging massive VCF files into a single VCF file or TPED file. Source codes can be slightly modified to fit into other types of sorted merging of Omics data. | compression, converge, merge, data, software, vcf, tped, conversion, file | Free, Available for download | SCR_016051 | 2026-09-05 06:30:07 | 1 | |||||||||||
|
University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility Resource Report Resource Website |
University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility (RRID:SCR_017144) | UKE Bioinformatics Core | access service resource, analysis service resource, core facility, production service resource, service resource, training service resource | Core provides bioinformatics services for researchers at University Medical Center Hamburg Eppendorf and related institutions. Focusing on high throughput sequencing data. Services include data analysis, consulting, software development, and bioinformatical training. | bioinformatics, data, analysis, consulting, software, development, training | has parent organization: University Medical Center Hamburg-Eppendorf | Restricted | SCR_017144 | Bioinformatics Core, University Medical Center Hamburg Eppendorf Core, UKE | 2026-09-05 06:30:08 | 0 | ||||||||
|
DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences. | evaluate, de novo, transcriptome, assembly, RNAseq, data, RSEM-EVAL, REF-EVAL, dataset, genomic, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NHGRI R01 HG005232; NLM T15 LM007359 |
PMID:25608678 | Free, Available for download, Freely available | biotools:detonate | https://bio.tools/detonate | SCR_017035 | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-09-05 06:30:08 | 2 | ||||
|
Brain Gene Expression Analysis toolbox Resource Report Resource Website 1+ mentions |
Brain Gene Expression Analysis toolbox (RRID:SCR_017438) | data analysis software, data processing software, software application, software resource | Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain. | Quantitative, analysis, digitized, brain, gene, expression, data, Allen Atlas, adult, mouse, brain, BRAIN Initiative |
is recommended by: BRAIN Initiative is related to: MATLAB is related to: Allen Institute for Brain Science works with: Allen Mouse Brain Reference Atlas |
Free, Available for download, Freely available | SCR_017438 | , Brain, Gene, Expression, Analysis, toolbox | 2026-09-05 06:30:09 | 1 | |||||||||
|
COVID-19 and Coronavirus plasmids and resources Resource Report Resource Website 1+ mentions |
COVID-19 and Coronavirus plasmids and resources (RRID:SCR_018347) | catalog, data or information resource, database | Collections of Addgene plasmids, open access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists. Ordering or depositing plasmids related to COVID-19 research. | Plasmid, COVID-19, SARS-CoV-2 plasmid, plasmid order, Adddgene, COVID-19 plasmid repository, COVID-19 related article, COVID-19 related protocol, COVID-19 resource collection, data | COVID-19 | Free, Freely available | SCR_018347 | 2026-09-05 06:30:09 | 1 | ||||||||||
|
Fitness Browser Resource Report Resource Website 1+ mentions |
Fitness Browser (RRID:SCR_018981) | data access protocol, data or information resource, software resource, web service | Web tool for browsing genome wide fitness experiments for diverse bacteria from Deutschbauer lab, the Arkin lab, and collaborators. Collection of mutant phenotypes for bacterial genes of unknown function. | Genome browser, bacteria, mutant phenotype, bacterial genes, unknown function, data | has parent organization: University of California at Berkeley; Berkeley; USA | NCRR S10 RR027303; NCRR S10 RR029668; NIH Office of the Director OD018174; Office of Science of the US Department of Energy |
PMID:29769716 | Free, Freely available | SCR_018981 | 2026-09-05 06:30:10 | 9 | ||||||||
|
cRAP protein sequences Resource Report Resource Website 100+ mentions |
cRAP protein sequences (RRID:SCR_018187) | cRAP | data or information resource, data repository, database, service resource, storage service resource | List of proteins commonly found in proteomics experiments that are present either by accident or through unavoidable contamination of protein samples. List is based on analysis of current version of GPMDB, as well as suggestions by users. Current version of cRAP in FASTA format can be obtained from the GPM FTP site. | Protein, collection, proteomic experiment, protein sample, contamination, Global Proteome Machine Data Base, data repository, data, FASEB list | THIS RESOURCE IS NO LONGER IN SERVICE | ftp://ftp.thegpm.org/fasta/cRAP | SCR_018187 | common Repository of Adventitious Proteins | 2026-09-05 06:30:09 | 198 | ||||||||
|
Loupe Browser Resource Report Resource Website 100+ mentions |
Loupe Browser (RRID:SCR_018555) | data analysis software, data processing software, software application, software resource | Desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Used to interrogate different views of 10x data to gain insights into underlying biology. | Interactive visualization, data analysis, 10x Genomics solutions, data | works with: Cell Ranger | Restricted | SCR_018555 | Loupe Cell Browser 4.0 | 2026-09-05 06:30:10 | 187 | |||||||||
|
Coronavirus Immunotherapy Consortium Resource Report Resource Website 10+ mentions |
Coronavirus Immunotherapy Consortium (RRID:SCR_018258) | CoVIC | consortium, data or information resource, organization portal, portal, topical portal | Consortium to unite efforts and resources from experts across globe to advance effective, antibody based therapies against novel coronavirus, SARS-CoV-2. Represents multidisciplinary convergence of structural biology, virologists, immunologists, clinicians and bioinformaticians from academic and industry settings. Collects antibodies for testing as part of CoVICS. Contributed antibodies are blinded and will only be known as code name. Antibody contributors will be able to see performance of their own molecules and take part in analysis. Contributors retain ownership of their antibodies and may continue to publish on them using original antibody names. Goal is to determine relative in vitro potency and in vivo efficacy using centralized standardized assays to identify best individual mAbs and rational combinations of mAbs. Consortium will recommend ideal therapeutic molecules for human use to protect vulnerable populations from COVID-19 disease. CoVIC database (CoVIC-DB) will serve as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. | COVID-19, antibody, antibody based therapy, coronavirus, SARS-CoV-2, antibody collection, analysis, potency in vitro, efficacy in vivo, standardized assay, identify mAb, therapeutic molecule, vulnerable population protect, database, data |
is related to: La Jolla Institute for Immunology is related to: Duke University; North Carolina; USA is related to: CoVIC-DB Database |
COVID-19 | Free, Freely available | SCR_018258 | 2026-09-05 06:30:09 | 14 | ||||||||
|
METAGENOTE Resource Report Resource Website 1+ mentions |
METAGENOTE (RRID:SCR_018494) | data access protocol, software resource, web service | Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository. | Annotate data, genomics study, microbiome, metadata, genomics, data |
is related to: NCBI Sequence Read Archive (SRA) is related to: NCBI |
NIH | Free, Freely available | SCR_018494 | METAdata of GEnomics studies on a web based NOTEbook | 2026-09-05 06:30:10 | 1 | ||||||||
|
Stanford University Human Immune Monitoring Center Core Facility Resource Report Resource Website 1+ mentions |
Stanford University Human Immune Monitoring Center Core Facility (RRID:SCR_018266) | HIMC | access service resource, core facility, data or information resource, service resource | Core designed for immune monitoring services for clinical and translational studies. Goals include providing standardized, state-of-the art immune monitoring assays at RNA, protein, and cellular level, testing and developing new technologies for immune monitoring, archive, report, and mine data from immune monitoring studies. HIMC uses online database for integration of data from standard HIMC assays, along with de-identified clinical and demographic data. | Immune monitoring serivce, clinical study, translational study, RNA, protein, data, core facility, USEDit, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Stanford University; Stanford; California |
Open | ABRF_399 | https://coremarketplace.org/?FacilityID=399 | SCR_018266 | Stanford University - Human Immune Monitoring Center, Human Immune Monitoring Center (HIMC) | 2026-09-05 06:30:09 | 1 | ||||||
|
Optimus Pipeline Resource Report Resource Website 1+ mentions |
Optimus Pipeline (RRID:SCR_018908) | data analysis software, data processing software, software application, software resource | Optimus is a pipeline developed by the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA) Project that supports processing of any 3' single-cell and single-nuclei expression data generated with the 10x Genomic v2 or v3 assay. It is an alignment and transcriptome quantification pipeline that corrects cell barcodes, aligns reads to the genome, corrects Unique Molecular Identifiers (UMIs), generates an expression matrix in a UMI-aware manner, calculates summary metrics for genes and cells, detects empty droplets, returns read outputs in BAM format, and returns gene counts in NumPy matrix and Loom matrix formats. | Data, single cell data, 10x technology data, cell bar code correction pipeline, reads alignment, genome, unique molecular identifier correction, mouse data sets analysis, human data sets analysis, |
is used by: BICCN is related to: Human Cell Atlas |
Free, Available for download, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/optimus | SCR_018908 | Optimus | 2026-09-05 06:30:10 | 2 | ||||||||
|
ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | data access protocol, service resource, software resource, web service | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R01 GM061867; NIGMS R35 GM118078 |
PMID:28079879 | Free, Freely available | SCR_018248 | ClusPro 2.0 | 2026-09-05 06:30:09 | 979 |
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.
