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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CummeRbund Resource Report Resource Website 100+ mentions |
CummeRbund (RRID:SCR_014568) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions. | r software, cufflink, rna-seq, sqlite, gene, transcript, transcription start site, cds region, r, rnaseq, rna seq, bio.tools, FASEB list |
uses: R Project for Statistical Computing is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; has parent organization: Harvard University; Cambridge; United States |
Free, Freely available | biotools:cummerbund, OMICS_07349 | https://bio.tools/cummerbund, https://sources.debian.org/src/r-bioc-cummerbund/ | SCR_014568 | SciCrunch Registry | 2026-10-31 12:16:15 | 366 | ||||||||
|
MicrobiomeUtilities Resource Report Resource Website 1+ mentions |
MicrobiomeUtilities (RRID:SCR_014611) | data analysis software, data processing software, sequence analysis software, software application, software resource | A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology. | microbiome, utilities, srna, 16s, nast alignment, chimera checking |
is listed by: Human Microbiome Project is listed by: Debian is listed by: OMICtools |
DOI:10.1101/gr.112730.110 | Available for download | OMICS_16932 | http://microbiomeutil.sourceforge.net, https://sources.debian.org/src/microbiomeutil/ | SCR_014611 | SciCrunch Registry | Microbiome Utilities Portal of the Broad Institute | 2026-10-31 12:16:24 | 8 | ||||||
|
FastQC Resource Report Resource Website 10000+ mentions Rating or validation data |
FastQC (RRID:SCR_014583) | data analysis software, data management software, data processing software, software application, software resource | Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis. | quality control, sequence data, sequencing, analysis, data quality, pipeline, raw sequence data, modular set, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Open source, Available for download | biotools:fastqc, SCR_005539, OMICS_01043 | https://omictools.com/fastqc-tool, https://bio.tools/fastqc, https://sources.debian.org/src/fastqc/ | SCR_014583 | SciCrunch Registry | FastQC v0.11.5 | 2026-10-31 12:16:15 | 19827 | |||||||
|
GROMACS Resource Report Resource Website 5000+ mentions |
GROMACS (RRID:SCR_014565) | simulation software, software application, software resource, software toolkit | Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers. | simulation, molecular dynamics, software package, software toolkit, biochemical, molecule, protein, lipid, nucleic acid, bond interaction, bio.tools |
is used by: CHARMM-GUI is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ; Nvidia ; Stream Computing Performance Engineers ; Swedish eScience Research Center ; Swedish Foundation for International Cooperation in Research and Higher Education ; Swedish Foundation for Strategic Research ; Swedish National Infrastructure for Computing ; Swedish Research Council |
PMID:26620784 DOI:10.1016/0010-4655(95)00042-E |
Free, Available for download | biotools:gromacs, OMICS_05081 | https://bio.tools/gromacs, https://sources.debian.org/src/gromacs/, https://github.com/gromacs/gromacs | SCR_014565 | SciCrunch Registry | Gromacs | 2026-10-31 12:16:23 | 9367 | |||||
|
Seq-Gen Resource Report Resource Website 100+ mentions |
Seq-Gen (RRID:SCR_014934) | simulation software, software application, software resource | Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. | simulator, simulation software, molecular evolution, nucleotide, amino acid, sequence, phylogeny, phylogenetic tree |
is listed by: Debian is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Wellcome Trust ; BBSRC ; Fogarty ; The Royal Society |
DOI:10.1093/bioinformatics/13.3.235 | Available for download | OMICS_15373 | https://sources.debian.org/src/seq-gen/ | SCR_014934 | SciCrunch Registry | 2026-10-31 12:16:22 | 158 | ||||||
|
ChIP-Atlas Resource Report Resource Website 100+ mentions |
ChIP-Atlas (RRID:SCR_015511) | data or information resource, database, software resource, web application | Database for visualizing and making use of public ChIP-seq data. ChIP-Atlas covers almost all public ChIP-seq experiments and data submitted to the SRA (Sequence Read Archives) in NCBI, DDBJ, or ENA. | chip-seq, sequence read archive, sequencing, FASEB list |
is listed by: OMICtools has parent organization: Kyushu University; Fukuoka; Japan has parent organization: NBDC - National Bioscience Database Center |
Freely Available | SCR_015511 | SciCrunch Registry | 2026-10-31 12:16:22 | 477 | ||||||||||
|
openBIS Resource Report Resource Website 10+ mentions |
openBIS (RRID:SCR_011815) | openBIS | software resource | Software for an open, distributed system for managing biological information that supports biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: * High Content Screening * Proteomics * Deep Sequencing * Metabolomics |
is listed by: OMICtools has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:22151573 | OMICS_01009 | SCR_011815 | SciCrunch Registry | open Biology Information System | 2026-10-31 12:15:31 | 14 | ||||||||
|
Kalign Resource Report Resource Website 100+ mentions |
Kalign (RRID:SCR_011810) | Kalign | software resource | A fast and accurate multiple sequence alignment algorithm. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:16343337 DOI:10.1093/bioinformatics/btz795 |
Free | OMICS_00978, biotools:kalign | https://bio.tools/kalign, https://sources.debian.org/src/kalign/ | SCR_011810 | SciCrunch Registry | 2026-10-31 12:15:29 | 123 | ||||||
|
MAFFT Resource Report Resource Website 10000+ mentions |
MAFFT (RRID:SCR_011811) | MAFFT | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments. | alignment, amino acid, nucleotide, sequence, DNA, sequence alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
EMBL ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:12136088 PMID:17118958 PMID:16362903 PMID:15661851 PMID:18439255 PMID:23023983 DOI:10.1093/bib/bbn013 |
biotools:MAFFT, OMICS_00979 | https://www.ebi.ac.uk/Tools/msa/mafft/, https://www.genome.jp/tools-bin/mafft, https://myhits.isb-sib.ch/cgi-bin/mafft, https://bio.tools/MAFFT, https://sources.debian.org/src/mafft/ | SCR_011811 | SciCrunch Registry | Multiple Alignment using Fast Fourier Transform, MAFFT version 5, MAFFT version 7 | 2026-10-31 12:15:29 | 24687 | |||||
|
CGView Resource Report Resource Website 100+ mentions |
CGView (RRID:SCR_011779) | CGView | software resource | A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Alberta; Alberta; Canada |
DOI:10.1093/bioinformatics/bti054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00905, biotools:cgview | https://bio.tools/cgview, https://sources.debian.org/src/cgview/ | SCR_011779 | SciCrunch Registry | Circular Genome Viewer | 2026-10-31 12:15:30 | 310 | |||||
|
PSAR-Align Resource Report Resource Website 1+ mentions |
PSAR-Align (RRID:SCR_011814) | PSAR-Align | software resource | Software for improving multiple sequence alignment using probabilistic sampling. | c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24222208 | Free | OMICS_00987, biotools:psar | https://bio.tools/psar | SCR_011814 | SciCrunch Registry | PSAR-Align: improving multiple sequence alignment using probabilistic sampling | 2026-10-31 12:15:29 | 1 | |||||
|
Gaggle Resource Report Resource Website |
Gaggle (RRID:SCR_011780) | Gaggle | software resource | An open source software tool for visualizing high-density data plotted against coordinates on the genome. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Open unspecified license, Free | biotools:ggb, OMICS_00909 | https://bio.tools/ggb | SCR_011780 | SciCrunch Registry | 2026-10-31 12:15:28 | 0 | |||||||
|
HiTEC Resource Report Resource Website 1+ mentions |
HiTEC (RRID:SCR_011826) | HiTEC | software resource | Accurate error correction in high-throughput sequencing data. | is listed by: OMICtools | OMICS_01105 | SCR_011826 | SciCrunch Registry | 2026-10-31 12:15:29 | 6 | ||||||||||
|
PatMaN Resource Report Resource Website 50+ mentions |
PatMaN (RRID:SCR_011821) | PatMaN | software resource | Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | c++, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18467344 DOI:10.1093/bioinformatics/btn223 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00997, biotools:patman | https://bio.tools/patman, https://sources.debian.org/src/patman/ | SCR_011821 | SciCrunch Registry | PatMaN - A DNA pattern matcher for short sequences | 2026-10-31 12:15:30 | 61 | |||||
|
Hammer Resource Report Resource Website 100+ mentions |
Hammer (RRID:SCR_011825) | Hammer | software resource | A tool for error correction of short read datasets with non-uniform coverage, such as single-cell data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
PMID:21685062 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01103 | SCR_011825 | SciCrunch Registry | Hammer: error correction with non-uniform coverage | 2026-10-31 12:15:29 | 196 | |||||||
|
Genome Projector Resource Report Resource Website 1+ mentions |
Genome Projector (RRID:SCR_011790) | Genome Projector | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk. | genome, plasmid, pathway, dna, map, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Japan Society for the Promotion of Science | GNU General Public License, V.2 | OMICS_00912, biotools:genome_projector | https://bio.tools/genome_projector | SCR_011790 | SciCrunch Registry | 2026-10-31 12:15:30 | 3 | ||||||
|
GNomEx Resource Report Resource Website 1+ mentions |
GNomEx (RRID:SCR_011805) | GNomEx | data repository, service resource, storage service resource | A Genomic Laboratory Information Management System (LIMS) and Data repository that can function as an experiment tracking and workflow management system for Core Facilities as well as an advanced data repository for storing and sharing genomic data sets. |
is listed by: OMICtools has parent organization: University of Utah; Utah; USA |
PMID:20828407 | OMICS_01005 | https://uofuhealth.utah.edu/huntsman/shared-resources/gba/bioinformatics/software/ | http://hci-scrum.hci.utah.edu/gnomexdoc/ | SCR_011805 | SciCrunch Registry | 2026-10-31 12:15:29 | 5 | |||||||
|
Infernal Resource Report Resource Website 500+ mentions |
Infernal (RRID:SCR_011809) | Infernal | software resource | Software for searching DNA sequence databases for RNA structure and sequence similarities. | FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: ANNOgesic has parent organization: Janelia Research |
PMID:24008419 DOI:10.1093/bioinformatics/btp157 |
GNU General Public License, v3 | OMICS_00977 | https://sources.debian.org/src/infernal/ | SCR_011809 | SciCrunch Registry | Infernal: inference of RNA alignments, INFERence of RNA Alignment | 2026-10-31 12:15:30 | 772 | |||||
|
GenomeMatcher Resource Report Resource Website 50+ mentions |
GenomeMatcher (RRID:SCR_011800) | GenomeMatcher | software resource | A graphical interface for comparative genomics. | is listed by: OMICtools | OMICS_00936 | SCR_011800 | SciCrunch Registry | 2026-10-31 12:15:30 | 65 | ||||||||||
|
GenomeRing Resource Report Resource Website 1+ mentions |
GenomeRing (RRID:SCR_011801) | GenomeRing | software resource | Alignment visualization based on SuperGenome coordinates. |
is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
OMICS_00937 | SCR_011801 | SciCrunch Registry | 2026-10-31 12:15:29 | 2 |
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
