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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
pearson-central-end-point Resource Report Resource Website |
pearson-central-end-point (RRID:SCR_016034) | data acquisition software, data processing software, data storage software, software application, software resource | Data collection software as an end-point for centrally storing data from the Pearsons Q-Interactive. | data, collection, end-point, central, storage, Pearson Q-Interactive, electronic, abcd | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016034 | 2026-09-19 12:55:15 | 0 | |||||||||
|
GeMoMa Resource Report Resource Website 100+ mentions |
GeMoMa (RRID:SCR_017646) | simulation software, software application, software resource | Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species. | Homology, based, gene, prediction, model, target, evolutionary, related, reference, species, sequence, conservation, intron, position, RNAseq, data, protein, coding, transcript, bio.tools |
is listed by: bio.tools is listed by: Debian works with: GUSHR |
PMID:31020559 | Free, Available for download, Freely available | biotools:gemoma | https://bio.tools/gemoma | SCR_017646 | Gene Model Mapper | 2026-09-19 12:55:17 | 158 | ||||||
|
BioDepot-workflow-builder Resource Report Resource Website 1+ mentions |
BioDepot-workflow-builder (RRID:SCR_017402) | Bwb | data processing software, software application, software resource, workflow software | Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results. | bioinformatics, big, data, workflow, reproducible, Docker | NHGRI U24HG012674; NHLBI U54 HL127624; NIAID R03AI159286; NIGMS R01 GM126019 |
DOI:10.1016/j.cels.2019.08.007 | Free, Available for download, Freely available | SCR_017402 | 2026-09-19 12:55:17 | 2 | ||||||||
|
dMRIPrep Resource Report Resource Website |
dMRIPrep (RRID:SCR_017412) | 3d spatial image, data analysis software, data or information resource, data processing software, diffusion-weighted mri 3d image, image, image processing software, mri 3d image, software application, software resource | Software tool as preprocessing pipeline for diffusion MRI. Pipeline used for preprocessing of diverse dMRI data. Workflow dispenses of manual intervention, thereby ensuring reproducibility of results. | Preprocessing, diffusion, MRI, imaging, data | Free, Available for download, Freely available | https://doi.org/10.5281/zenodo.3392201 | SCR_017412 | 2026-09-19 12:55:17 | 0 | ||||||||||
|
MrDiffusion Resource Report Resource Website 1+ mentions |
MrDiffusion (RRID:SCR_016567) | data analysis software, data processing software, data visualization software, image analysis software, software application, software resource | Software package for diffusion imaging analysis and visualization. Module of Vistasoft for processing diffusion weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, RGB fiber direction maps and analysis of MRI data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | diffusion, imaging, analysis, visualization, data, fractional, anisotropy, MRI |
is related to: MATLAB has parent organization: Stanford University; Stanford; California |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/vistalab/vistasoft/tree/master/mrDiffusion | SCR_016567 | 2026-09-19 12:55:16 | 9 | |||||||||
|
CMap Resource Report Resource Website 500+ mentions |
CMap (RRID:SCR_016204) | data or information resource, data set, database, software resource, web application | Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines. | data, set, connectivity, gene, expression, database, heat map, drug, tool, perturbational, perturbagen, signature, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Free for academic use, Subscription for commercial use, Available for download, Acknowledgement requested | biotools:CMap | https://bio.tools/CMap | SCR_016204 | LINCS CMap L1000, LINCS L1000, LINCS CMap, ConnectivityMap, Connectivity Map | 2026-09-19 12:55:16 | 789 | |||||||
|
fastp Resource Report Resource Website 1000+ mentions |
fastp (RRID:SCR_016962) | data analysis software, data processing software, software application, software resource | Software tool to provide fast all in one preprocessing for FastQ files. Developed in C++ with multithreading supported to afford high performance. Performs quality control, adapter trimming, quality filtering, per read quality pruning and many other operations with a single scan of the FASTQ data. | fast, all in one, preprocessing, FastQ, file, data, read, quality, control, adapter, trimming, filtering | is listed by: OMICtools | National Science Foundation of China ; Special Funds for Future Industries of Shenzhen |
PMID:30423086 | Free, Available for download, Freely available | SCR_016962 | 2026-09-19 12:55:16 | 1745 | ||||||||
|
RecView Resource Report Resource Website 1+ mentions |
RecView (RRID:SCR_016531) | data processing software, image analysis software, image processing software, image reconstruction software, software application, software resource | Software tool as a program for tomographic reconstruction and image processing of micro/nano-CT data taken at SPring8 and APS Argonne. | computational, tomographic, reconstruction, image, processing, micro, nano, CT, data | Japan Society for the Promotion of Science | Free, Available for download, Freely available | SCR_016531 | 2026-09-19 12:55:16 | 4 | ||||||||||
|
Spyder Resource Report Resource Website 50+ mentions |
Spyder (RRID:SCR_017585) | software application, software development environment, software development tool, software resource | Interactive scientific development environment package for Python. Used for editing, analysis, debugging, and profiling functionality of comprehensive development tool with data exploration, interactive execution, deep inspection, and visualization. | Python, environment, editing, analysis, debugging, profiling, functionality, development, data, exploration, visualization | is related to: Pythonxy | Free, Available for download, Freely available | SCR_017585 | 2026-09-19 12:55:17 | 75 | ||||||||||
|
SMARTdenovo Resource Report Resource Website 100+ mentions |
SMARTdenovo (RRID:SCR_017622) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as de novo assembler for PacBio and Oxford Nanopore data. It produces assembly from all-vs-all raw read alignments without error correction stage. Allows to read overlapping, rescue missing overlaps, identify low-quality regions and chimaera and produce better consensus. | De novo, assembler, PacBio, Oxford Nanopore, data, sequence, raw, read, alignment, error, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:SMARTdenovo, biotools:SMARtdenovo | https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo | SCR_017622 | 2026-09-19 12:55:17 | 191 | ||||||||
|
duphold Resource Report Resource Website 1+ mentions |
duphold (RRID:SCR_016938) | data analysis software, data processing software, software application, software resource | Software tool to annotate structural variant calls with sequence depth information that can add or remove confidence to SV predicted to affect copy number. Indicates the presence of a rapid change in depth relative to the regions surrounding the breakpoints. Allows the run time to be nearly independent of the number of variants important for large, jointly called projects with many samples. Annotates structural variant predictions made from both short read and long read data. | annotate, structural, variation, call, sequence, depth, confidence, predict, copy, number, short, long, read, data | is listed by: OMICtools | Free, Available for download, Freely available | SCR_016938 | 2026-09-19 12:55:16 | 3 | ||||||||||
|
UMMPerfusion Resource Report Resource Website 1+ mentions |
UMMPerfusion (RRID:SCR_015970) | data processing software, image analysis software, software application, software resource, software toolkit | Analysis software for dynamic contrast enhanced magnetic resonance images with implementation of a pixel-by-pixel deconvolution approach. It quantifies T1-weighted contrast-enhanced dynamic MR imaging (DCE-MRI) perfusion data as an OsiriX plug-in. | DCE-MRI, t1, weighted, imaging, mr, magnetic, resonance, analysis, digital, perfusion, parameter, data, set, image, algorithm, contrast, pixel | is affiliated with: Heidelberg University; Baden-Wurttemberg; Germany | Heinrich-Vetter-Stiftung | PMID:22832894 | Open source, Available for download, Runs on Mac OS, Tutorial available | SCR_015970 | OsiriX plugin | 2026-09-19 12:55:15 | 6 | |||||||
|
GENIST Resource Report Resource Website 1+ mentions |
GENIST (RRID:SCR_016942) | data analysis software, data processing software, software application, software resource | Software tool as an algorithm to infer gene regulatory networks from spatial and temporal datasets. Spatial dataset or any data that can provide information about coexpression is used by the first step of the algorithm to perform clustering and separate the genes in the network in smaller coexpressed groups. Temporal dataset is used by the second step of the algorithm to infer regulations among the genes, based on Bayesian networks. | infer, gene, regulatory, network, spatial, temporal, dataset, data, coexpression, clustering, separate, Bayesian | Free, Available for download, Freely available | https://github.com/madeluis/GENIST/commits/master | SCR_016942 | Gene Regulatory Network Inference | 2026-09-19 12:55:16 | 1 | |||||||||
|
redcap-hook-framework Resource Report Resource Website |
redcap-hook-framework (RRID:SCR_016028) | data management software, software application, software resource | Software tool to organize and deploy custom hooks in a single project or across the entire instance. It features multi-language support for data entry and survey pages, a bar-code for text fields, and highlighting of rows on data entry and survey pages that have been filled out. | data, organize, deploy, custom, hooks, project, abcd, adolescence | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016028 | 2026-09-19 12:55:15 | 0 | |||||||||
|
QModeling Resource Report Resource Website 1+ mentions |
QModeling (RRID:SCR_016358) | data analysis software, data processing software, image analysis software, software application, software resource, software toolkit | Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences. | statistical, parametric, mapping, reference, region, kinetic, model, dynamic, analysis, brain, data, imaging, sequence |
is related to: University of Malaga; Andalusia; Spain is related to: MATLAB |
DOI:10.1007/s12021-018-9384-y | Free, Available for download, Available after registration | SCR_016358 | 2026-09-19 12:55:16 | 1 | |||||||||
|
CloudMerge Resource Report Resource Website 1+ mentions |
CloudMerge (RRID:SCR_016051) | data compression software, data processing software, software application, software resource, source code | Software for merging massive VCF files into a single VCF file or TPED file. Source codes can be slightly modified to fit into other types of sorted merging of Omics data. | compression, converge, merge, data, software, vcf, tped, conversion, file | Free, Available for download | SCR_016051 | 2026-09-19 12:55:15 | 1 | |||||||||||
|
University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility Resource Report Resource Website |
University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility (RRID:SCR_017144) | UKE Bioinformatics Core | access service resource, analysis service resource, core facility, production service resource, service resource, training service resource | Core provides bioinformatics services for researchers at University Medical Center Hamburg Eppendorf and related institutions. Focusing on high throughput sequencing data. Services include data analysis, consulting, software development, and bioinformatical training. | bioinformatics, data, analysis, consulting, software, development, training | has parent organization: University Medical Center Hamburg-Eppendorf | Restricted | SCR_017144 | Bioinformatics Core, University Medical Center Hamburg Eppendorf Core, UKE | 2026-09-19 12:55:17 | 0 | ||||||||
|
DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences. | evaluate, de novo, transcriptome, assembly, RNAseq, data, RSEM-EVAL, REF-EVAL, dataset, genomic, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NHGRI R01 HG005232; NLM T15 LM007359 |
PMID:25608678 | Free, Available for download, Freely available | biotools:detonate | https://bio.tools/detonate | SCR_017035 | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-09-19 12:55:16 | 2 | ||||
|
Brain Gene Expression Analysis toolbox Resource Report Resource Website 1+ mentions |
Brain Gene Expression Analysis toolbox (RRID:SCR_017438) | data analysis software, data processing software, software application, software resource | Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain. | Quantitative, analysis, digitized, brain, gene, expression, data, Allen Atlas, adult, mouse, brain, BRAIN Initiative |
is recommended by: BRAIN Initiative is related to: MATLAB is related to: Allen Institute for Brain Science works with: Allen Mouse Brain Reference Atlas |
Free, Available for download, Freely available | SCR_017438 | , Brain, Gene, Expression, Analysis, toolbox | 2026-09-19 12:55:17 | 1 | |||||||||
|
COVID-19 and Coronavirus plasmids and resources Resource Report Resource Website 1+ mentions |
COVID-19 and Coronavirus plasmids and resources (RRID:SCR_018347) | catalog, data or information resource, database | Collections of Addgene plasmids, open access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists. Ordering or depositing plasmids related to COVID-19 research. | Plasmid, COVID-19, SARS-CoV-2 plasmid, plasmid order, Adddgene, COVID-19 plasmid repository, COVID-19 related article, COVID-19 related protocol, COVID-19 resource collection, data | COVID-19 | Free, Freely available | SCR_018347 | 2026-09-19 12:55:18 | 1 |
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
