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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | software application, data processing software, data analysis software, sequence analysis software, software resource, software toolkit | Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning. | analysis, genetic, sequence, multiply, alignment, rate, pattern, data, evolution, platform, python, r, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NSF DBI-0096033; NSF DEB-9996118; NIH R01 AI47745; NIH U01 AI43638; University of California Universitywide AIDS Research Program IS02-SD-701; University of California ; San Diego Center for AIDS Research/NIAID Developmental Award 2 P30 AI36214; NIGMS R01 |
PMID:15509596 | Free, Available for download, Freely available | SCR_016271, biotools:HyPhy, OMICS_04235 | https://sources.debian.org/src/hyphy-pt/ https://veg.github.io/hyphy-site/ https://github.com/veg/hyphy https://bio.tools/HyPhy |
SCR_016162 | HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt | 2026-02-17 10:02:39 | 1497 | |||||
|
zUMIs Resource Report Resource Website 100+ mentions |
zUMIs (RRID:SCR_016139) | data analysis software, software application, data processing software, software resource | Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information. | single-cell, RNA-seq, UMI, Genomics, shell, r, perl, rna, cdna, cell, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/153940 | Open source, Free, Available for download | biotools:zumis | https://bio.tools/zumis | SCR_016139 | zumi | 2026-02-17 10:02:39 | 118 | ||||||
|
BioPlex Resource Report Resource Website 1000+ mentions |
BioPlex (RRID:SCR_016144) | storage service resource, data or information resource, database, service resource, data repository | Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection. | cell, line, protein, immunopurification, mass, spectrometry, interaction, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard Medical School; Massachusetts; USA |
NHGRI U41HG006673; NIDDK K01 DK098285; Canadian Institutes for Health Research |
PMID:28514442 | biotools:bioplex_2.0 | https://bio.tools/bioplex_2.0 | SCR_016144 | BioPlex (biophysical interactions of ORFeome-based complexes), Harvard BioPlex, Biophysical Interactions of Orfeome-based comPLEXes (BioPLEX) | 2026-02-17 10:02:39 | 1355 | ||||||
|
mentha Resource Report Resource Website 100+ mentions |
mentha (RRID:SCR_016148) | software application, web application, data or information resource, data processing software, data analysis software, database, software resource | Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. | protein, ppi, imex, interactome, archival, bio.tools, FASEB list |
uses: PSICQUIC Registry is listed by: Debian is listed by: bio.tools is related to: IMEx - The International Molecular Exchange Consortium |
PMID:23900247 | biotools:mentha, r3d100011124 | https://bio.tools/mentha https://doi.org/10.17616/R3SP8V |
SCR_016148 | 2026-02-17 10:03:22 | 149 | ||||||||
|
FluxModeCalculator Resource Report Resource Website 1+ mentions |
FluxModeCalculator (RRID:SCR_016290) | data analysis software, software application, data processing software, software resource | Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | efm, flux, stoichiometry, algorithm, matlab, linux, model, magnitude, bio.tools |
is listed by: Debian is listed by: bio.tools |
Netherlands Consortium for Systems Biology (NCSB) ; Center of Medical Systems Biology (CMSB) ; European Network for Genetic and Genomic Epidemiology (ENGAGE) ; Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) ; CardioVascular Research Netherlands (CVON-ENERGISE) |
PMID:26685305 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fluxmodecalculator, OMICS_10894 | https://bio.tools/fluxmodecalculator | SCR_016290 | Flux Mode Calculator | 2026-02-17 10:02:40 | 1 | |||||
|
Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | data management software, software application, production service resource, analysis service resource, software resource, service resource, data analysis service | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | 2026-02-17 10:03:01 | 2 | |||||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | software application, data processing software, data analysis software, software resource, software toolkit | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-02-17 10:03:01 | 5 | |||||||
|
DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | software application, web application, data processing software, data analysis software, software resource, sequence analysis software | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | Drug target Interaction Network Inference Engine based on Supervised analysis | 2026-02-17 10:03:27 | 4 | ||||
|
SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | software application, data processing software, data analysis software, software resource, software toolkit | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-02-17 10:03:23 | 2 | |||||
|
MentaLiST Resource Report Resource Website 1+ mentions |
MentaLiST (RRID:SCR_016469) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome Canada ; Genome BC |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-02-17 10:03:27 | 8 | ||||||
|
cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | image processing software, software application, data processing software, software resource | Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. | data, processing, high, resolution, electron, cryo, macroscopy, single, particle, averaging, image, macromolecule, high, resolution, 3D, bio.tools |
is listed by: bio.tools is listed by: Debian |
Howard Hughes Medical Institute | DOI:10.7554/eLife.35383 | Open source, Trial available | biotools:cistem | https://bio.tools/cistem | SCR_016502 | computational imaging system for Transmission Electron Microscopy | 2026-02-17 10:03:02 | 64 | ||||
|
Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | web application, production service resource, analysis service resource, service resource, software resource, data analysis service | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/ https://bio.tools/pavian |
SCR_016679 | 2026-02-17 10:03:04 | 22 | ||||||
|
Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | software application, image processing software, standalone software, data processing software, data analysis software, software resource, data visualization software | Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. | segmentation, analysis, multidimentional, dataset, light, electron, microscopy, image, processing, visualization, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: MATLAB |
Biocenter Finland ; Biological Imaging Network Academy of Finland ; University of Helsinki |
PMID:26727152 | Free, Available for download, Freely available | biotools:mib | https://www.youtube.com/watch?v=I9FWmJX_nl0&index=1&list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj https://bio.tools/mib |
SCR_016560 | MIB, Microscopy Image Browser | 2026-02-17 10:03:28 | 143 | ||||
|
Centrifuge Classifier Resource Report Resource Website 1+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
U. S. Army Research Office W911NF1410490; NSF ABI1356078; NHGRI R01 HG006677; NIGMS R01 GM083873 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge https://bio.tools/centrifuge https://sources.debian.org/src/centrifuge/ |
SCR_016665 | 2026-02-17 10:02:44 | 9 | ||||||
|
TB PORTALS Resource Report Resource Website 10+ mentions |
TB PORTALS (RRID:SCR_016594) | organization portal, storage service resource, data or information resource, topical portal, consortium, disease-related portal, service resource, portal, data repository | Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data. | collect, data, sharing, analysis, tuberculosis, global, bio.tools |
is listed by: NIAID is listed by: bio.tools is listed by: Debian |
tuberculosis | NIH | DOI:10.1128/JCM.01013-17 | Free, Freely available | r3d100013925, biotools:TB_Portals | https://bio.tools/TB_Portals https://doi.org/10.17616/R31NJN8L |
SCR_016594 | 2026-02-17 10:02:43 | 12 | |||||
|
NMRProcFlow Resource Report Resource Website 10+ mentions |
NMRProcFlow (RRID:SCR_016592) | data visualization software, software application, data processing software, software resource | Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics. | NMR, metabolomics, data, viewer, spectra, processing, graphical, interface, bio.tools |
uses: R Project for Statistical Computing is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
French National Infrastructure in Metabolomics and Fluxomics | DOI:10.1007/s11306-017-1178-y | Free, Available for download, Freely available | biotools:nmrprocflow, SCR_022777 | https://github.com/INRA/NMRProcFlow https://bio.tools/nmrprocflow https://github.com/inra/nmrprocflow |
SCR_016592 | Nuclear Magnetic Resonance PROcessing FLOW, Nuclear Magnetic Resonance Processing Flow | 2026-02-17 10:03:26 | 23 | |||||
|
CheckM Resource Report Resource Website 100+ mentions |
CheckM (RRID:SCR_016646) | software application, data processing software, data analysis software, software resource, software toolkit | Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. | assess, quality, microbial, genome, recovered, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/gr.186072.114 | Free, Available for download, Freely available | biotools:checkm | https://github.com/Ecogenomics/CheckM https://bio.tools/checkm |
SCR_016646 | 2026-02-17 10:02:44 | 184 | |||||||
|
Genotyping Resource Report Resource Website 10+ mentions |
Genotyping (RRID:SCR_016645) | data access protocol, software application, data processing software, data analysis software, software resource, web service, sequence analysis software | Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus. | identify, genotype, viral, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI works with: NCBI BLAST |
Free, Freely available | biotools:ncbi_genotyping | https://bio.tools/ncbi_genotyping | SCR_016645 | 2026-02-17 10:03:27 | 31 | ||||||||
|
Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | software application, data processing software, data analytics software, data analysis software, software resource, sequence analysis software | Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. | gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF 1640775 | Free, Available for download, Freely available | biotools:Libra_k-mer | https://bio.tools/Libra_k-mer | SCR_016608 | 2026-02-17 10:03:28 | 0 | |||||||
|
kallisto Resource Report Resource Website 100+ mentions |
kallisto (RRID:SCR_016582) | data analysis software, software application, data processing software, software resource | Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads. | bio.tools |
is listed by: Debian is listed by: bio.tools works with: sleuth works with: kb_python |
PMID:27043002 | Free, Available for download, Freely available | biotools:kallisto | https://pachterlab.github.io/kallisto/download.html https://bio.tools/kallisto https://sources.debian.org/src/kallisto/ |
SCR_016582 | kallisto v0.43.1 | 2026-02-17 10:03:03 | 127 |
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
Email: info_at_ dknet.org
