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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Rolexa Resource Report Resource Website 1+ mentions |
Rolexa (RRID:SCR_013017) | Rolexa | software resource | Software that provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01156 | SCR_013017 | SciCrunch Registry | 2026-10-10 12:39:11 | 1 | ||||||||||
|
TraceTuner Resource Report Resource Website 10+ mentions |
TraceTuner (RRID:SCR_013019) | TraceTuner | software resource | Software tool for base and quality calling of trace files from DNA sequencing instruments. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
Free | OMICS_01158 | https://sources.debian.org/src/tracetuner/ | SCR_013019 | SciCrunch Registry | TraceTuner - DNA sequencing quality values base calling and trace processing | 2026-10-10 12:39:01 | 14 | |||||||
|
GenomeView Resource Report Resource Website 10+ mentions |
GenomeView (RRID:SCR_012968) | GenomeView | data or information resource, database, software resource | A next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. | is listed by: OMICtools | PMID:22102585 | OMICS_00913 | SCR_012968 | SciCrunch Registry | 2026-10-10 12:38:59 | 36 | |||||||||
|
seqMINER Resource Report Resource Website 100+ mentions |
seqMINER (RRID:SCR_013020) | seqMINER | software resource | Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq). | java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21177645 | GNU General Public License, v3 | biotools:seqminer, OMICS_00460 | https://bio.tools/seqminer | SCR_013020 | SciCrunch Registry | 2026-10-10 12:39:19 | 190 | ||||||
|
MIREAP Resource Report Resource Website 100+ mentions |
MIREAP (RRID:SCR_013025) | MIREAP | software resource | A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00376 | SCR_013025 | SciCrunch Registry | 2026-10-10 12:39:01 | 389 | |||||||||
|
MIReNA Resource Report Resource Website 1+ mentions |
MIReNA (RRID:SCR_013024) | MIReNA | software resource | A software tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. | is listed by: OMICtools | PMID:20591903 | Acknowledgement requested, CeCILL license | OMICS_00377 | SCR_013024 | SciCrunch Registry | 2026-10-10 12:38:57 | 8 | ||||||||
|
MIG Resource Report Resource Website 1+ mentions |
MIG (RRID:SCR_012972) | MIG | software resource | Allows the user to conveniently compare data from many loci., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00942 | SCR_012972 | SciCrunch Registry | Multi-Image Genome | 2026-10-10 12:38:59 | 1 | ||||||||
|
Behavioral Risk Factor Surveillance System Resource Report Resource Website 100+ mentions |
Behavioral Risk Factor Surveillance System (RRID:SCR_012974) | data or information resource, disease-related portal, portal, research forum portal, topical portal | The Behavioral Risk Factor Surveillance System (BRFSS) is a state-based system of health surveys that collects information on health risk behaviors, preventive health practices, and health care access primarily related to chronic disease and injury. For many states, the BRFSS is the only available source of timely, accurate data on health-related behaviors. BRFSS was established in 1984 by the Centers for Disease Control and Prevention (CDC); currently data are collected monthly in all 50 states, the District of Columbia, Puerto Rico, the U.S. Virgin Islands, and Guam. More than 350,000 adults are interviewed each year, making the BRFSS the largest telephone health survey in the world. States use BRFSS data to identify emerging health problems, establish and track health objectives, and develop and evaluate public health policies and programs. Many states also use BRFSS data to support health-related legislative efforts. Sponsors: This resource is supported by the Center for Disease Control. Keywords: Behavioral, Risk, Factor, Surveillance, System, Health, Disease, Chronic, Injury, Health, Behavior, Health, | has parent organization: Centers for Disease Control and Prevention | nif-0000-30157 | SCR_012974 | SciCrunch Registry | BRFSS | 2026-10-10 12:39:10 | 327 | ||||||||||
|
EDNA Resource Report Resource Website 10+ mentions |
EDNA (RRID:SCR_012981) | EDNA | software resource | Software for Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23990411 | Creative Commons Attribution NonCommercial License, v2 | OMICS_00974 | SCR_012981 | SciCrunch Registry | EDNA - Energy Based Multiple Sequence Alignment (MSA) for Binding Sites | 2026-10-10 12:39:00 | 34 | ||||||
|
cn.mops Resource Report Resource Website 10+ mentions |
cn.mops (RRID:SCR_013036) | cn.mops | software resource | A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
biotools:cn.mops, OMICS_00335 | https://bio.tools/cn.mops | SCR_013036 | SciCrunch Registry | Copy Number estimation by a Mixture Of PoissonS | 2026-10-10 12:39:01 | 10 | |||||||
|
SAMZIP Resource Report Resource Website |
SAMZIP (RRID:SCR_012980) | SAMZIP | software resource | An encoding and decoding tool for Sequence Alignment/Map (SAM) files. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22164252 | OMICS_00967 | SCR_012980 | SciCrunch Registry | 2026-10-10 12:38:56 | 0 | |||||||||
|
TopHat Resource Report Resource Website 5000+ mentions Rating or validation data |
TopHat (RRID:SCR_013035) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. | align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools |
uses: Bowtie is used by: CIRCexplorer is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: HISAT2 has parent organization: University of Maryland; Maryland; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Johns Hopkins University; Maryland; USA has parent organization: University of Washington; Seattle; USA works with: GeneScissors |
NHGRI R01 HG006102; NHGRI R01 HG006677 |
PMID:23618408 PMID:19289445 DOI:10.1093/bioinformatics/btp120 |
Free, Available for download, Freely available | biotools:tophat, OMICS_01257 | https://github.com/infphilo/tophat, https://bio.tools/tophat, https://sources.debian.org/src/tophat/ | http://tophat.cbcb.umd.edu/ | SCR_013035 | SciCrunch Registry | tophat, TopHat1, Tophat2 | 2026-10-10 12:38:57 | 9789 | ||||
|
Virus Pathogen Resource (ViPR) Resource Report Resource Website 100+ mentions |
Virus Pathogen Resource (ViPR) (RRID:SCR_012983) | ViPR | data or information resource, data processing software, data repository, data visualization software, database, service resource, software application, software resource, storage service resource | Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research. | flu, gene, bioinformatic, database, diagnostic, genomic, health, human, influenza, pathogen, protein, research, strain, therapeutic, tool, vaccine, virus, visualization, FASEB list |
is recommended by: National Library of Medicine is listed by: Data and Computational Resources to Address COVID-19 is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: University of Texas Southwestern Medical Center; Texas; USA |
COVID-19 | NIAID | Restricted | nif-0000-25312, DOI:10.35083, DOI:10.35084, DOI:10.17616/R30P93, DOI:10.25504/FAIRsharing.2qx8n8 | http://www.viprbrc.org/, https://doi.org/10.17616/r30p93, https://doi.org/10.35083/, https://doi.org/10.35084/, https://dx.doi.org/10.35083/, https://dx.doi.org/10.35084/, https://fairsharing.org/10.25504/FAIRsharing.2qx8n8 | SCR_012983 | SciCrunch Registry | Virus Pathogen Resource, ViPR | 2026-10-10 12:39:10 | 173 | ||||
|
SAMMate Resource Report Resource Website 10+ mentions |
SAMMate (RRID:SCR_013037) | SAMMate | software resource | An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
biotools:sammate, OMICS_01264 | https://bio.tools/sammate | SCR_013037 | SciCrunch Registry | 2026-10-10 12:39:20 | 11 | ||||||||
|
Flexbar Resource Report Resource Website 100+ mentions |
Flexbar (RRID:SCR_013001) | Flexbar | software resource | Flexible barcode and adapter removal for sequencing platforms. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.3390/biology1030895 | biotools:flexbar | https://bio.tools/flexbar, https://sources.debian.org/src/flexbar/ | SCR_013001 | SciCrunch Registry | 2026-10-10 12:38:57 | 307 | |||||||
|
Mobyle@Pasteur Resource Report Resource Website 100+ mentions |
Mobyle@Pasteur (RRID:SCR_013089) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A portal for bioinformatics analyses, including the following: alignment assembly database display genetics hmm information nucleic phylogeny protein sequence structure | FASEB list | has parent organization: Pasteur Institute | nlx_156919 | SCR_013089 | SciCrunch Registry | Mobyle@Pasteur | 2026-10-10 12:39:21 | 203 | |||||||||
|
Cochrane Library Resource Report Resource Website 10000+ mentions |
Cochrane Library (RRID:SCR_013000) | Cochrane Library | data or information resource, database | Contains data to inform healthcare decision-making from Cochrane and other systematic reviews, clinical trials, and more. Cochrane reviews bring you the combined results of the worlds best medical research studies, and are recognized as the gold standard in evidence-based health care. Consists of a regularly updated collection of evidence-based medicine databases, including The Cochrane Database of Systematic Reviews. This database includes systematic reviews of healthcare interventions that are produced and disseminated by The Cochrane Collaboration. It is published on a monthly basis and made available both on CD-ROM and the Internet. The review abstracts are available to browse and search free of charge on this website. The Cochrane Library Users'' Group (CLUG) provides a forum for discussion of usability, readability, searchability, and formatting issues related to the use of The Cochrane Library. The Cochrane Collaboration is an international not-for-profit and independent organization, dedicated to making up-to-date, accurate information about the effects of healthcare readily available worldwide. Funded by John Wiley and Sons Limited. The individual entities of The Cochrane Collaboration are funded by a large variety of governmental, institutional and private funding sources, and are bound by organisation-wide policy limiting uses of funds from corporate sponsors. | clinical trial, decision, healthcare, medical, medicine, research, scientific literature databases and services, systematic, FASEB list | is related to: Covidence | nif-0000-21389 | SCR_013000 | SciCrunch Registry | The Cochrane Library, Cochrane Library | 2026-10-10 12:39:10 | 40628 | ||||||||
|
GenomeRNAi Resource Report Resource Website 100+ mentions |
GenomeRNAi (RRID:SCR_013088) | data or information resource, data repository, database, service resource, storage service resource | GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome | drosophila genome, caenorhabditis elegans, caenorhabditis elegans genome, c. elegans, drosophila, drosophila cells, human genome, rnai |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases has parent organization: German Cancer Research Center |
nif-0000-02901, r3d100011089 | https://www.ncbi.nlm.nih.gov/gap | SCR_013088 | SciCrunch Registry | GenomeRNAi, Genome RNAi | 2026-10-10 12:39:02 | 385 | ||||||||
|
SHREC Resource Report Resource Website 10+ mentions |
SHREC (RRID:SCR_013009) | SHREC | software resource | A bioinformatics tool for error correction of HTS read data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01110 | SCR_013009 | SciCrunch Registry | 2026-10-10 12:39:01 | 14 | ||||||||||
|
hiCtools Resource Report Resource Website |
hiCtools (RRID:SCR_013010) | hiCtools | software resource | This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_00522 | SCR_013010 | SciCrunch Registry | 2026-10-10 12:39:19 | 0 |
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 U24DK097771.
Email: info_at_ dknet.org
