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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
bioSyntax Resource Report Resource Website 1+ mentions |
bioSyntax (RRID:SCR_016207) | data management software, software application, software resource | Software for syntax highlighting for computational biology. | computation, syntax, language, code, scientific, data, workflow, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
DOI:10.1186/s12859-018-2315-y | Free, Available for download | biotools:biosyntax, OMICS_25594 | https://github.com/bioSyntax/bioSyntax, https://bio.tools/biosyntax, https://sources.debian.org/src/biosyntax/ | SCR_016207 | SciCrunch Registry | 2026-10-24 12:47:33 | 2 | |||||||
|
IDEPI - IDentify EPItopes Resource Report Resource Website |
IDEPI - IDentify EPItopes (RRID:SCR_016171) | software library, software resource, software toolkit | IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application. | modeling, machine, learning, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:25254639 | Free, Available for download | biotools:idepi | https://bio.tools/idepi | SCR_016171 | SciCrunch Registry | 2026-10-24 12:47:33 | 0 | |||||||
|
odMLtables Resource Report Resource Website 1+ mentions |
odMLtables (RRID:SCR_016228) | data management software, data processing software, data visualization software, software application, software resource | Software that facilitates the handling of metadata collections stored in the odML format. Some supported operations include reduction, merging of odml structures, and the conversion from the hierarchical odML format to tabular formats. | metadata, collection, odml, hierarchy, tabular structure, markup language, data management, graph, spreadsheet, bio.tools |
uses: Open metadata mark up language is listed by: Debian is listed by: bio.tools |
PMID:31611781 | Free, Available for download, Tutorial available | biotools:odMLtables | https://github.com/INM-6/python-odmltables, https://bio.tools/odMLtables | SCR_016228 | SciCrunch Registry | odML-tables, odML tables | 2026-10-24 12:47:33 | 2 | ||||||
|
ASHLAR Resource Report Resource Website 1+ mentions |
ASHLAR (RRID:SCR_016266) | Ashlar | data processing software, image processing software, software application, software resource | Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration. | cycif, registration, software, python, cyclic, immunofluorescence, fluorescence, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM107618 | Free, Available for download | biotools:ASHLAR | https://bio.tools/ASHLAR | SCR_016266 | SciCrunch Registry | ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration | 2026-10-24 12:47:38 | 6 | |||||
|
tensorflow Resource Report Resource Website 500+ mentions |
tensorflow (RRID:SCR_016345) | software library, software resource, software toolkit | Software as an open source machine learning framework for everyone. Library for high performance numerical computation. Allows deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. | high, performance, numerical, computation, machine, learning, framework, everyone, bio.tools |
is used by: transfer_ learning_ ccnn is listed by: Debian is listed by: bio.tools is related to: PPR-Meta is related to: PySyft is related to: Rosetta is related to: tf-encrypted |
Free, Available for download, Freely available | biotools:tensorflow | https://github.com/tensorflow/tensorflow, https://bio.tools/tensorflow, https://sources.debian.org/src/libtensorflow-framework2/ | SCR_016345 | SciCrunch Registry | 2026-10-24 12:47:38 | 724 | ||||||||
|
MGnify Resource Report Resource Website 50+ mentions |
MGnify (RRID:SCR_016429) | data or information resource, data repository, portal, service resource, storage service resource | Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020. | analysis, exploration, metagenomic, metatranscriptomic, amplicon, assembly, data, sequence, ENA, microbial, population, environment, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Debian is listed by: bio.tools is related to: NIDDK Information Network (dkNET) |
EMBL ; EU Seventh Framework Programme for Research MICROB3; InnovateUK 102513; Research Councils UK (RCUK) ; the Biotechnology and Biological Sciences Research Council (BBSRC) BBM0117551; the Biotechnology and Biological Sciences Research Council (BBSRC) BBN0183541; the Biotechnology and Biological Sciences Research Council BBI02612X1; the Biotechnology and Biological Sciences Research Council BBM0117551; the European Commission within the Research Infrastructures programme of Horizon 2020 676559 |
PMID:31696235 | Free, Freely available, Training online available | r3d100011192, biotools:MGnify | https://bio.tools/MGnify, https://doi.org/10.17616/R34W68 | SCR_016429 | SciCrunch Registry | , MGnify, EBI Metagenomics | 2026-10-24 12:47:36 | 74 | |||||
|
GEO2R Resource Report Resource Website 50+ mentions |
GEO2R (RRID:SCR_016569) | data analysis software, data processing software, software application, software resource | Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance. | compare, group, sample, gene, expression, omnibus, data, identify, differentially, expressed, across, condition, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: GEOquery is related to: LIMMA |
Free, Available for download, Freely available | biotools:GEO2R | https://bio.tools/GEO2R | SCR_016569 | SciCrunch Registry | 2026-10-24 12:47:38 | 76 | ||||||||
|
Splicing Express Resource Report Resource Website 1+ mentions |
Splicing Express (RRID:SCR_016498) | data analysis software, data processing software, data visualization software, software application, software resource | Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems. | alternative, splicing, analysis, next, generation, sequencing, data, transcriptome, identify, annotate, visualize, Perl, UNIX, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:26618088 | Free, Available for download, Freely available | biotools:splicing_express | https://bio.tools/splicing_express | SCR_016498 | SciCrunch Registry | 2026-10-24 12:47:37 | 3 | |||||||
|
SARTools Resource Report Resource Website 100+ mentions |
SARTools (RRID:SCR_016533) | data analysis software, data processing software, software application, software resource, software toolkit | Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data. | R package, DESeq2, EdgeR, comprehensive, analysis, RNAseq, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: DESeq2 is related to: edgeR has parent organization: Pasteur Institute |
the France Génomique National Infrastructure | PMID:27280887 | Free, Available for download, Freely available | biotools:sartools | https://bio.tools/sartools | SCR_016533 | SciCrunch Registry | 2026-10-24 12:47:39 | 151 | ||||||
|
TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_016492) | data analysis software, data processing software, software application, software resource | Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. | statistical, analysis, TnSeq, data, identify, gene, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Texas A and M University; Texas; USA |
PMID:26447887 | Free, Available for download, Freely available | biotools:transit | https://github.com/mad-lab/transit, https://bio.tools/transit | SCR_016492 | SciCrunch Registry | 2026-10-24 12:47:37 | 4 | |||||||
|
ANOCVA Resource Report Resource Website |
ANOCVA (RRID:SCR_016719) | ANOCVA | data analysis software, data processing software, software application, software resource | Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders. | nonparametric, statistical, test, compare, clustering, structure, functional, brain, network, magnetic, resonance, imaging, data, fMRI, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: CRAN |
CAPES and CNPq Fellowships ; Ciência sem Fronteiras Fellowship ; NAP eScience ; Pew Latin American Fellowship ; State of São Paulo Research Foundation |
PMID:28174516 | Free, Available for download, Freely available | biotools:anocva | https://bio.tools/anocva | SCR_016719 | SciCrunch Registry | ANalysis Of Cluster VAriability, Analysis of Cluster Variability | 2026-10-24 12:47:40 | 0 | ||||
|
CARD Resource Report Resource Website 10+ mentions |
CARD (RRID:SCR_016602) | CARD | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, web application | Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data. | integrated, analysis, interactive, visualization, RNA, interfernce, screening, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Australasian Genomics Technologies Association ; Australian Cancer Research Foundation ; Australian Government’s Education Investment Fund ; Brockhoff Foundation ; Peter MacCallum Cancer Centre Foundation ; Victorian Department of Industry ; Innovation and Regional Development |
PMID:26902267 | Free, Freely available | biotools:CARD | https://bio.tools/CARD | SCR_016602 | SciCrunch Registry | CARD, Comprehensive Analysis of RNAi-screen Data | 2026-10-24 12:47:38 | 20 | ||||
|
VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses. | visual, framework, analysis, sequencing, data, dataset, integrative, interactive, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor |
Canadian Institutes of Health Research (CIHR) and Genome BC ; Michael Smith Foundation for Health Research ; NSERC PGS-D |
PMID:26328469 | Free, Available for download, Freely available | biotools:VisR | https://bio.tools/VisR | SCR_016658 | SciCrunch Registry | VisRseq, VisR | 2026-10-24 12:47:39 | 5 | ||||
|
IndelGenotyper Resource Report Resource Website 50+ mentions |
IndelGenotyper (RRID:SCR_016663) | GATK | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer. | next, generation, analysis, genomic, data, cancer, genome |
is listed by: Debian has parent organization: Broad Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/broadinstitute/gatk/, https://sources.debian.org/src/gatk/ | SCR_016663 | SciCrunch Registry | GATK Indel Genotyper, Genome Analysis Toolkit (GATK) Indel Genotyper, Indel Genotyper, GATK IndelGenotyper | 2026-10-24 12:47:39 | 88 | |||||||
|
biobakery Resource Report Resource Website 10+ mentions |
biobakery (RRID:SCR_016596) | data analysis software, data processing software, software application, software resource, software toolkit | Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Huttenhower lab, metaomics, data, analysis, process, raw, shotgun, metagenome, metatranscriptome, sequencing, microbial, profiling, bio.tools |
is used by: Nephele is listed by: Debian is listed by: bio.tools is related to: Human Microbiome Project has parent organization: Harvard University; Cambridge; United States |
ARO W911NF1110473; NHGRI R01 HG005220; NHGRI R01 HG005969; NIDDK U54 DE023798; NSF DBI1053486; Sloan Foundation 4406J0B |
PMID:29194469 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biobakery | http://huttenhower.sph.harvard.edu/biobakery, https://bio.tools/biobakery | SCR_016596 | SciCrunch Registry | bioBakery, biobakery | 2026-10-24 12:47:38 | 18 | |||||
|
PhenoMeNal Resource Report Resource Website 1+ mentions |
PhenoMeNal (RRID:SCR_016605) | phnmnl, PhenoMeNal | consortium, data access protocol, data or information resource, organization portal, portal, software resource, web service | Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics. | metabolomic, phenomic, data, processing, analysis, information, mining. medical, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory has parent organization: European Bioinformatics Institute |
European Commission EC654241 | Free, Registration required, Tutorial available | biotools:PhenoMeNal | https://github.com/phnmnl, https://bio.tools/PhenoMeNal | SCR_016605 | SciCrunch Registry | Phenome and Metabolome aNalysis | 2026-10-24 12:47:38 | 3 | |||||
|
SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | data analysis software, data processing software, data visualization software, software application, software resource | Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically. | data, mining, visualization, analysis, polychromatic, flow, cytometry, dataset, normalized, graphically, bio.tools |
is listed by: NIAID is listed by: Debian is listed by: bio.tools |
NIAID ; NIH |
PMID:21265010 | Free, Available for download, Freely available | biotools:spice | https://bio.tools/spice | SCR_016603 | SciCrunch Registry | Simplified Presentation of Incredibly Complex Evaluations | 2026-10-24 12:47:38 | 72 | ||||
|
OmicsNet Resource Report Resource Website 50+ mentions |
OmicsNet (RRID:SCR_016724) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web based tool to create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space (genes/proteins, microRNAs, transcription factors or metabolites). | create, molecular, interaction, network, visually, 3D, gene, protein, microRNA, transcription factor, metabolite, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Canada Research Chairs Program ; Genome Canada ; Natural Sciences and Engineering Research Council of Canada |
PMID:29878180 | Free, Freely available | biotools:omicsnet | https://bio.tools/omicsnet | SCR_016724 | SciCrunch Registry | 2026-10-24 12:47:40 | 52 | ||||||
|
SCIPION Resource Report Resource Website 10+ mentions |
SCIPION (RRID:SCR_016738) | data processing software, image processing software, software application, software resource, software toolkit | Software framework for image processing to obtain 3D models of macromolecular complexes using Electron Microscopy. Open-source project for integration, reproducibility and validation in 3D electron microscopy. It integrates several software packages to execute workflows combining different software tools, while taking care of formats and conversions. Electron Microscopy (3DEM). waiting for pdf from Joe | image, processing, data, 3DEM, macromolecular, complex, electron, microscopy, format, conversion, bio.tools |
is listed by: bio.tools is listed by: Debian |
Comunidad the Madrid ; European Union ; Instruct ; Spanish Ministry of Economy and Competitiveness |
PMID:27108186 | Free, Available for download, Registration required | biotools:monores | https://github.com/I2PC/scipion, https://bio.tools/monores | SCR_016738 | SciCrunch Registry | 2026-10-24 12:47:40 | 21 | ||||||
|
Metascape Resource Report Resource Website 1000+ mentions |
Metascape (RRID:SCR_016620) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies. | analyze, gene, protein, list, data, annotate, resource, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:Metascape | https://bio.tools/Metascape | SCR_016620 | SciCrunch Registry | 2026-10-24 12:47:39 | 3966 |
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.
