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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CRISPRdirect Resource Report Resource Website 500+ mentions |
CRISPRdirect (RRID:SCR_018186) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. | CRISP/Cas guide RNA, reduced off target site, design of CRISP/Cas target, selecting rational target, sequence, genomic sequence, RNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Japan Science and Technology Agency ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:25414360 | Free, Freely available | biotools:CRISPRdirect | https://bio.tools/CRISPRdirect | SCR_018186 | SciCrunch Registry | 2026-10-10 12:40:15 | 588 | ||||||
|
NBRP Medaka Pattern Match Resource Report Resource Website 1+ mentions |
NBRP Medaka Pattern Match (RRID:SCR_018157) | analysis service resource, data or information resource, database, production service resource, service resource | Web medaka pattern match tool for short sequence and/or pattern. Used to search database of medaka genome on target and off target sites when editing genome with CRISRP-Cas9. | Medaka, pattern match tool, short sequence, pattern, medaka genome, target site, off target site, editing genome, CRISP-Cas9 | has parent organization: Kyoto University; Kyoto; Japan | Free, Freely available | SCR_018157 | SciCrunch Registry | 2026-10-10 12:40:10 | 5 | ||||||||||
|
Mizar Imaging: Tilt High Resolution Light Sheet Imaging System Resource Report Resource Website |
Mizar Imaging: Tilt High Resolution Light Sheet Imaging System (RRID:SCR_018156) | instrument resource | Modular light sheet illumination system designed to image living samples with minimal photobleaching or phototoxicity by Mizar Imaging. Enables high spatial and temporal resolution light sheet imaging to be added to existing or new microscope system. | Mizar Imaging, light sheet imaging, modular homology, illumination system, image living sample, minimal photobleaching, minimal phototoxicity, microscope system, instrument, equipment | Restricted | https://www.mizarimaging.com/wp-content/uploads/2018/11/Tilt-Datasheet-3.pdf | SCR_018156 | SciCrunch Registry | Tilt | 2026-10-10 12:40:10 | 0 | |||||||||
|
S2 Genomics: Singulator 100 Automated Single Cell Prep Automated System Resource Report Resource Website 1+ mentions |
S2 Genomics: Singulator 100 Automated Single Cell Prep Automated System (RRID:SCR_018155) | instrument resource | Singulator to automate tissue preparation for single cell and single nucleus analyses. Bench top Singulator System and single use cartridge enable tissue dissociations into singulated cells or nuclei suspensions. | S2 Genomics, automated cell preparation, tissue preparation, single cell, single nucleus analysis, benchtop, singulator system, single use cartridge, singulated cell suspension, singulated nuclei suspension, instrument, equipment | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018155.pdf | https://s2genomics.com/wp-content/uploads/2022/08/S2-Genomics-Singulator-100-Brochure-v220804.pdf | SCR_018155 | SciCrunch Registry | S2 Genomics Singulator, S2 Genomics Singulator 100, Singulator 100 | 2026-10-10 12:40:15 | 2 | ||||||||
|
YXLON: FF35 CT Resource Report Resource Website 1+ mentions |
YXLON: FF35 CT (RRID:SCR_018208) | instrument resource | Computed tomography system designed to achieve precise inspection results for wide range of applications by YXLON. Available in single or dual tube configuration, it is perfect for very small to medium sized parts inspection in automotive, electronics, aviation, and material science industries. | Computed tomography system, instrument, equipment | Restricted | https://etek-aero.com/wp-content/uploads/2022/09/FF35-CT_Brochure_en-LR-1.pdf | SCR_018208 | SciCrunch Registry | 2026-10-10 12:40:16 | 1 | ||||||||||
|
Black Zen software Resource Report Resource Website 100+ mentions |
Black Zen software (RRID:SCR_018163) | data processing software, image analysis software, image processing software, software application, software resource | Software used to analyze images obtained from microscope. ZEN Black is software Zeiss uses to run their laser-based instruments. | Free, Available for download, Freely available | http://microscopy.arizona.edu/sites/default/files/sites/default/files/upload/Installing%20the%20free%20Zeiss%20ZEN%20software%20on%20a%20Windows%20PC%20%28rev2018%29.pdf | SCR_018163 | SciCrunch Registry | ZEISS ZEN Microscope Software, Black Zen software (ZEISS), ZEN Black | 2026-10-10 12:40:15 | 169 | ||||||||||
|
NeMO Analytics Resource Report Resource Website 10+ mentions |
NeMO Analytics (RRID:SCR_018164) | analysis service resource, data analysis service, data or information resource, portal, production service resource, service resource, topical portal | Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools. | Visualization, analysis, multi omic data, cell type, developing brain, adult brain, RNAseq, ATACseq, CHIPseq, fetal human prefrontal cortex, stem cell, neural induction, brain, data |
is used by: BICCN is related to: NeMOarchive is related to: BRAIN Initiative is related to: Brainome portal is related to: BRAIN Initiative Cell Atlas Network |
Free, Freely available | SCR_018244 | SCR_018164 | SciCrunch Registry | Neuroscience Multi-Omic Analytics | 2026-10-10 12:40:10 | 16 | ||||||||
|
Eppendorf: 5920R centrifuge Resource Report Resource Website 1+ mentions |
Eppendorf: 5920R centrifuge (RRID:SCR_018092) | instrument resource | Swinging bucket benchtop centrifuge. Eppendorf 5920 R refrigerated centrifuge. | Centrifuge, swinging bucket, benchtop, Eppendorf, refrigerated centrifuge, instrument, equipment | Restricted | https://www.eppendorf.com/product-media/doc/en/330744/Centrifugation_Operating-manual_Centrifuge-5920-R.pdf | SCR_018092 | SciCrunch Registry | 2026-10-10 12:40:09 | 1 | ||||||||||
|
Fcirc Resource Report Resource Website 1+ mentions |
Fcirc (RRID:SCR_018090) | Fcirc | data processing software, software application, software resource, workflow software | Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs. | Fusion gene, linear and circular RNA, fusion exploration, RNAseq data, linear transcript, circRNA, gene, data, pipeline, bio.tools |
uses: HISAT2 uses: SAMTOOLS is listed by: Debian is listed by: bio.tools |
National Key Research and Development Program 2017YFC0908500 ; National Natural Science Foundation of China 31571363 ; National Natural Science Foundation of China 31771469 ; National Natural Science Foundation of China 81573023 |
Free, Available for download, Freely available | biotools:Fcirc | https://bio.tools/Fcirc | SCR_018090 | SciCrunch Registry | Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs | 2026-10-10 12:40:51 | 2 | |||||
|
HingeProt Resource Report Resource Website 1+ mentions |
HingeProt (RRID:SCR_018136) | data access protocol, service resource, software resource, web service | Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures. | Predicting protein hinges, flexible hinge region, native topology, rigid protein part, elastic network model, protein structure, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17847101 | Free, Available for download, Freely available | biotools:hingeprot | https://bio.tools/hingeprot | SCR_018136 | SciCrunch Registry | 2026-10-10 12:40:10 | 4 | |||||||
|
Beckman Coulter: Biomek i7 Hybrid Automated Workstation Resource Report Resource Website 1+ mentions |
Beckman Coulter: Biomek i7 Hybrid Automated Workstation (RRID:SCR_018094) | instrument resource | Liquid handling instrument designed to optimize dependability and walk-away time. Biomek i7 Hybrid with enclosure has up to 45 deck positions and includes both Multichannel and Span-8 pipette heads in enclosed work space. | Liquid handling, instrument, equipment, Beckman Coulter | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018094.pdf | https://bec-techdocs-prod.s3.us-west-2.amazonaws.com/techdoc/files/ifu/en/C16028AB.pdf?AWSAccessKeyId=ASIA2KJI7HMZ33DV6WQG&Expires=1701735968&Signature=2MDYEbJhW4PJy4sgXzeeS9DyO%2B8%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEP%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJGMEQCIHg6cmtDSAztedNNXtxyHC%2FQ9o4yM1SgSuLP9xeBShEqAiBzvdXKsSIHPDhKAAp89Ph3a%2F5N4WI6Q%2B2vzPWAUmArISr6AghoEAQaDDcwOTI5MjQwNzYwMyIMCupsWUjiXR86CzK6KtcCan1TNZecdLIPuEOW2TsrPrXuHumQlBikN6ce3yhHyhkat%2BXxcoT72Pefl%2FuXb8zIanpeQ2sRYiTG8XuuwjK%2B016PUCUcgWG%2FUbf4t2y12I2SLOd3YI%2FgEHK7sPoIpH2K4tkz%2FVPXgRQ8zMgYMsMSq2XxD%2F2iGkromeIhZvz1a12ertzuOrynkyfT%2FZFAWt0p2NADzT%2F8kc3WLrWByJbzv6vmPs4%2ByZPUdva6vQ6dM2F0%2F9L%2BRULmL8RsHpbOfslrhsEZY9BK%2FuoSx49fTTyKmKPs8g%2FDthw5g6r7YhAzTWk0cVagwcSRZ%2F7xdsjhGusWmQNJvFfNyz72rvaddAINSSLWsjArEdL2NUZahdlFZ%2BzbyqAC3thGwmySgtkHdEVSWmqPHvZ9o80lR9seE1mXvIVtc%2FLW2LVl76gjIxRcND2QtTZKw5CpR%2F8YtYDKySe4eBxtZux8HTD8rbmrBjqfAfP6m3jf8H5DybTLXkGz6gxd3X4fRRuizXOxQGkUA3whw298yFHAZWDEBP3LUp0cL6rJFdjvd7oEJ44qaZRNwKUtjYjk9%2FviPVWPPsZCX%2BIvmEE%2FN77lL6Dav6ASE8fjWuS3V8hnTTbo%2Filx%2F18BNJZIJ1ftJuUMhizI75F9CvvnLtweybGFoajnIOBQkN1ArufaYn%2BGCQPsVh1TOR%2F8Fw%3D%3D | SCR_018094 | SciCrunch Registry | 2026-10-10 12:40:51 | 7 | |||||||||
|
seaborn Resource Report Resource Website 100+ mentions |
seaborn (RRID:SCR_018132) | data processing software, data visualization software, software application, software library, software resource, software toolkit | Software Python tool as data visualization library based on matplotlib. Provides interface for drawing attractive and informative statistical graphics. Statistical data visualization using matplotlib. | Data visualization library, statistical graphic, statistical data visualization | uses: Matplotlib | Free, Available for download, Freely available | https://github.com/mwaskom/seaborn/tree/v0.10.0 | SCR_018132 | SciCrunch Registry | 2026-10-10 12:40:10 | 479 | |||||||||
|
Anatomography Resource Report Resource Website 1+ mentions |
Anatomography (RRID:SCR_018147) | service resource, software resource, web application | Web application that enables users to build and publish own custom manikins. Used to build three dimensional model of human body using parts registered in BodyParts3D. Server returns image of assembled 3D model as still image, rotating animation, interactive image, etc. Each part can be downloaded as polygon mesh file that can be used with 3D printer. | Custom manikins, 3D, body parts, three dimensional model, human body, image, rotating animation, interactive image, BodyParts3D, 3D printer | Free, Freely available | SCR_018147 | SciCrunch Registry | BodyParts3D / Anatomography | 2026-10-10 12:40:10 | 6 | ||||||||||
|
ChromHMM Resource Report Resource Website 50+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, data processing software, software application, software resource | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
Alfred P. Sloan Fellowship ; CAREER Award ; NHGRI RC1HG005334; NHGRI U01 HG007912; NHGRI U54 HG004570; NIEHS R01 ES024995; NIMH U01 MH105578; NSF 0905968 |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | SciCrunch Registry | 2026-10-10 12:40:15 | 50 | ||||||
|
Warp Resource Report Resource Website 10+ mentions |
Warp (RRID:SCR_018071) | data acquisition software, data analysis software, data processing software, software application, software resource | Software tool that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Corrects micrographs for global and local motion, estimates local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. Software includes deep-learning-based models for accurate particle picking and image denoising. | Automating preprocessing step, cryo EM data acquisition, micrograph correction, particle picking, image denoising, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1038/s41592-019-0580-y | Free, Available for download, Freely available | BioTools:Warp, biotools:Warp | https://bio.tools/Warp, https://bio.tools/Warp, https://bio.tools/Warp | SCR_018071 | SciCrunch Registry | 2026-10-10 12:40:09 | 10 | |||||||
|
gProfiler2 Resource Report Resource Website 50+ mentions |
gProfiler2 (RRID:SCR_018190) | data analysis software, data processing software, software application, software resource | Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool. | Gene list, functional enrichment analysis, namespace conversion, data, analysis |
is listed by: ELIXIR Tools and Data Services Registry is related to: R Project for Statistical Computing works with: g:Profiler |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:31066453 | Free, Available for download, Freely available | SCR_018190 | SciCrunch Registry | gprofiler2 | 2026-10-10 12:40:52 | 63 | |||||||
|
Agisoft Metashape Resource Report Resource Website 100+ mentions |
Agisoft Metashape (RRID:SCR_018119) | data processing software, image processing software, software application, software resource, standalone software | Stand alone software that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales. Successor of PhotoScan and is advanced image-based 3D modeling solution aimed at creating professional quality 3D content from still images. | Agisoft LLC, photogrammetry processing, digital image, 3D spatial data, GIS, visual effect production, 3D computer graphic |
is related to: Agisoft Photoscan is related to: Agisoft Photoscan |
SCR_018119 | SciCrunch Registry | 2026-10-10 12:40:09 | 172 | |||||||||||
|
RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | data access protocol, simulation software, software application, software resource, web service | Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model. | Protein structure predictor, 3D structure, protein sequence, secondary and tertiary structure, binding site, solvent accessibility, disordered region, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
NIGMS R01 GM089753; NSF DBI 0960390 |
PMID:21987485 | Restricted | biotools:raptorx | https://bio.tools/raptorx | SCR_018118 | SciCrunch Registry | 2026-10-10 12:40:14 | 198 | ||||||
|
QIIME 2 View Resource Report Resource Website 100+ mentions |
QIIME 2 View (RRID:SCR_018074) | data acquisition software, data processing software, data visualization software, service resource, software application, software resource | Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided. | QIIME 2, visualization, data, interface, file viewing, file download and displaying | Free, Freely available | https://github.com/qiime2/q2view | SCR_018074 | SciCrunch Registry | q2view | 2026-10-10 12:40:09 | 102 | |||||||||
|
FlowPy Resource Report Resource Website 1+ mentions |
FlowPy (RRID:SCR_018195) | data analysis software, data processing software, data visualization software, software application, software resource | Software Python tool for flow cytometry data. Data generated by flow cytometer can be read by FlowPy. Used for data extraction, data visualization, data clustering, histogram subtraction. | Flow cytometry data, data extraction, data visualization, data clustering, histogram subtraction | Free, Available for download, Freely available | SCR_018195 | SciCrunch Registry | 2026-10-10 12:40:10 | 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
