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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
rCASC Resource Report Resource Website 1+ mentions |
rCASC (RRID:SCR_017005) | data analysis software, data processing software, software application, software resource | Software package for reproducible classification analysis of single cell sequencing data. | reproducibility, classification, analysis, single, cell, sequencing, data, bio.tools |
is used by: Stardust is listed by: Debian is listed by: bio.tools is related to: University of Turin;Turin;Italy |
PMID:24204232 | Free, Available for download, Freely available | biotools:rCASC | https://kendomaniac.github.io/rCASC/, https://bio.tools/rCASC | SCR_017005 | SciCrunch Registry | rCASC, reproducible Cluster Analysis of Single Cells | 2026-10-17 01:29:13 | 1 | ||||||
|
INCF-Neurobot Resource Report Resource Website 10+ mentions |
INCF-Neurobot (RRID:SCR_017004) | INCF Neurobot | data management software, data processing software, software application, software resource | Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis. | data, management, clinical, study, brain, traumatic, injury |
has parent organization: Karolinska Institute; Stockholm; Sweden has parent organization: International Neuroinformatics Coordinating Facility |
Registration required | SCR_017004 | SciCrunch Registry | , International Neuroinformatics Coordinating Facility Neurobot, INCF Neurobot | 2026-10-17 01:29:37 | 17 | ||||||||
|
ImmuneDB Resource Report Resource Website 1+ mentions |
ImmuneDB (RRID:SCR_017125) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features. | collect, store, analysis, B cell, T cell, immune, receptor, sequencing, data, process, raw, read | is used by: AIRR Data Commons | NCI P30 CA016520; NIAID P01 AI106697; NIAID P30 AI0450080; NIDDK UC4 DK112217 |
PMID:30298069 | Free, Available for download, Freely available | https://github.com/arosenfeld/immunedb | SCR_017125 | SciCrunch Registry | 2026-10-17 01:29:39 | 8 | |||||||
|
Stemformatics Resource Report Resource Website 1+ mentions |
Stemformatics (RRID:SCR_017002) | data or information resource, data set, organization portal, portal, service resource | Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data. Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others. | gene, expression, data, stem, cell, community, microarray, RNA, sequencing, dataset, cluster | ARC Discovery Project ; ARC Future Fellowship ; ARC Special Research Initiative to Stem Cells Australia ; JEM Research Foundation philanthropic funding ; QLD Government Smart Futures Fellowship ; University of Melbourne Centre for Stem Cell Systems |
PMID:23466562 | Free, Available for download, Freely available | SCR_017002 | SciCrunch Registry | 2026-10-17 01:29:11 | 1 | |||||||||
|
CATALYST Resource Report Resource Website 100+ mentions |
CATALYST (RRID:SCR_017127) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation. | preprocessing, cytometry, data, normalization, bead, standard, single, cell, deconvulsion, compensation, bio.tools |
uses: CATALYSTLite is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
European Research Council ; NIDDK UC4 DK108132; PhosphonetPPM and MetastasiX SystemsX grant ; Roche Postdoctoral Fellowship ; SNSF Assistant Professorship grant ; Swiss National Science Foundation |
PMID:29605184 | Free, Available for download, Freely available | biotools:catalyst | https://github.com/HelenaLC/CATALYST, https://bio.tools/catalyst | SCR_017127 | SciCrunch Registry | Cytometry dATa anALYSis Tools | 2026-10-17 01:29:14 | 241 | |||||
|
Scikit-Criteria Resource Report Resource Website |
Scikit-Criteria (RRID:SCR_017084) | software library, software resource, software toolkit | Software tool as collection of Multiple Criteria Decision Analysis methods integrated into scientific Python stack. | collection, multiple, criteria, decision, analysis, method, integrated, stack | is related to: Python Programming Language | Free, Available for download, Freely available | https://github.com/leliel12/scikit-criteria/blob/master/doc/source/index.rst, https://github.com/leliel12/scikit-criteria, | SCR_017084 | SciCrunch Registry | 2026-10-17 01:29:39 | 0 | |||||||||
|
Surface Modified Amperometry CMOS IC Resource Report Resource Website 1+ mentions |
Surface Modified Amperometry CMOS IC (RRID:SCR_017082) | instrument resource | Integrated circuit device used as tool for amperometry measurement as replacement of conventional carbon fiber microelectrode. Surface modified structures with SU 8 microwells increases life span of each individual device and achieves single cell measurement efficiency by trapping cells inside microwells. | instrument, device, CMOS, amperometry, measurement, chip, microelectrode, microwell, cell, semiconductor | PMID:28889250 | SCR_017082 | SciCrunch Registry | Surface Modified Amperometry Complementary Metal Oxide Semiconductor IC | 2026-10-17 01:29:12 | 1 | ||||||||||
|
SwiftOrtho Resource Report Resource Website 1+ mentions |
SwiftOrtho (RRID:SCR_017122) | data analysis software, data processing software, software application, software resource | Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets. | orthology, analysis, identify, ortholog, paralog, co ortholog, genome, homology, different, species, large, dataset, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/543223 | Free, Available for download, Freely available | OMICS_30890, biotools:SwiftOrtho | https://bio.tools/SwiftOrtho | SCR_017122 | SciCrunch Registry | 2026-10-17 01:29:22 | 4 | |||||||
|
Haystack Resource Report Resource Website 1+ mentions |
Haystack (RRID:SCR_017087) | data analysis software, data processing software, software application, software resource, software toolkit | Software suite of computational tools implemented in Python to study epigenetic variability, cross cell type plasticity of chromatin states and transcription factors motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation. Epigenetic variability and transcription factor motifs analysis pipeline. | epigenetic, variability, cell, plasticity, chromatin, transcription, factor, motif, structure, gene, regulation, analysis |
is related to: Python Programming Language has parent organization: Harvard University; Cambridge; Massachusetts |
Free, Available for download, Freely available | https://github.com/pinellolab/haystack_bio | SCR_017087 | SciCrunch Registry | haystack, haystack_bio | 2026-10-17 01:29:22 | 3 | ||||||||
|
cgpBattenberg Resource Report Resource Website 10+ mentions |
cgpBattenberg (RRID:SCR_017092) | data analysis software, data processing software, software application, software resource | Software tool as installation helper, perl wrapper and R program Battenberg which detects subclonality and copy number in matched NGS data. | installation, helper, perl, wrapper, detect, subclonality, copy, number, NGS, next, generation, sequencing, data | is related to: battenberg | Free, Available for download, Freely available | SCR_017092 | SciCrunch Registry | 2026-10-17 01:29:22 | 13 | ||||||||||
|
Flye Resource Report Resource Website 100+ mentions |
Flye (RRID:SCR_017016) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms. | assembler, single, molecule, sequencing, long, error, read, fast, accurate, genome, reconstruction, nucleotide, quality, data, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at San Diego; California; USA |
PMID:27956617 | Free, Available for download, Freely available | biotools:Flye | https://bio.tools/Flye, https://sources.debian.org/src/flye/ | SCR_017016 | SciCrunch Registry | 2026-10-17 01:29:37 | 324 | |||||||
|
Olympus: FluoView FV3000 Confocal Laser Scanning Microscope Resource Report Resource Website 50+ mentions |
Olympus: FluoView FV3000 Confocal Laser Scanning Microscope (RRID:SCR_017015) | instrument resource | FV3000 is a laser scanning confocal microscope system that captures high-resolution, high-contrast images by scanning samples point by point, enabling precise 3D fluorescence imaging. The system supports inverted and upright configurations and accommodates various objectives with magnifications ranging from 1.25× to 100×, including oil, silicone, and dry lenses, which allows imaging of both macro and micro-scale samples. It is equipped with multiple laser lines for excitation, including 405 nm, 488 nm, 561 nm, and 640 nm, as well as additional lines in some configurations (445 nm, 514 nm, 594 nm, 630 nm), enabling the use of several fluorophores simultaneously. On the detection side, the microscope uses high-sensitivity photomultiplier tube detectors, including GaAsP PMTs and multi-alkali PMTs. | instrument, Olympus, confocal, laser, scanning, microscope, Fluoview, FV3000 |
is used by: Texas State University Nanofabrication Research Service Center Core Facility is provided by: Olympus works with: Olympus FV31S-SW software |
Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_017015.pdf | https://www.olympus-global.com/technology/design/product/fv3000_series.html | https://www.olympus-lifescience.com/en/laser-scanning/fv3000 | SCR_017015 | SciCrunch Registry | , Olympus FV3000 Confocal, Olympus FV3000 microscope, FLUOVIEW FV3000 | 2026-10-17 01:29:11 | 57 | ||||||
|
Experimental Design Assistant Resource Report Resource Website 100+ mentions |
Experimental Design Assistant (RRID:SCR_017019) | EDA | service resource, software resource, web application | Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility. | in vivo, design, conduct, analysis, reporting, animal, experiment, irreproducibility, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NC3Rs |
PMID:28957312 | Free, Freely available | biotools:eda | https://bio.tools/eda | SCR_017019 | SciCrunch Registry | EDA, Experimental Design Assistant (EDA), Experimental Design Assistant | 2026-10-17 01:29:12 | 192 | |||||
|
LION/web Resource Report Resource Website 10+ mentions |
LION/web (RRID:SCR_017018) | Lipid Ontology (LION) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Web based ontology enrichment tool for lipidomic data analysis. Used for lipidomics to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and organelle associations. Freely accessible in a platform independent way. | lipid, ontology, enrichment, lipidomic, data, analysis, biophysical | is related to: Utrecht University; Utrecht; Netherlands | DOI:10.1101/398040 | Free, Freely available | SCR_017018 | SciCrunch Registry | The Lipid Ontology (LION), Lipid Ontology, LIpid ONtology (LION), LIpid ONtology, LION | 2026-10-17 01:29:21 | 33 | |||||||
|
Anima Resource Report Resource Website 10+ mentions |
Anima (RRID:SCR_017017) | 3d spatial image, data analysis software, data or information resource, data processing software, diffusion-weighted mri 3d image, image, image analysis software, image processing software, mri 3d image, portal, registration software, software application, software resource, software toolkit | Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows. | medical, image, processing, analysis, registration, statistical, quantitative, MRI, data, VISAGES |
is related to: Anima scripts is related to: Empenn has parent organization: VISAGES Research |
Free, Freely available, Available for download | http://olivier.commowick.org/software_anima.php | SCR_017017 | SciCrunch Registry | 2026-10-17 01:29:13 | 20 | |||||||||
|
dndSCV Resource Report Resource Website 10+ mentions |
dndSCV (RRID:SCR_017093) | data analysis software, data processing software, software application, software resource | Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets. | dN/dS, method, quantify, selection, cancer, somatic, evolution, missense, nonsense, essential, splice, mutation, gene, genome, dataset |
uses: devtools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017093 | SciCrunch Registry | 2026-10-17 01:29:12 | 36 | ||||||||||
|
GAGE Resource Report Resource Website 50+ mentions |
GAGE (RRID:SCR_017067) | data analysis software, data processing software, software application, software resource | Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies. | gene, set, enrichment, pathway, batch, comparison, parallel, analysis, heterogeneous, data |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017067 | SciCrunch Registry | Generally Applicable Gene-set Enrichment for pathway analysis, gage, Generally Applicable Gene-set Enrichment, GSEA | 2026-10-17 01:29:12 | 53 | |||||||||
|
Comparative Metatranscriptomics Workflow Resource Report Resource Website 1+ mentions |
Comparative Metatranscriptomics Workflow (RRID:SCR_017109) | CoMW | data analysis software, data or information resource, data processing software, narrative resource, sequence analysis software, software application, software resource, training material, workflow | Software tool for standardized and validated workflow to functionally classify quality filtered mRNA reads from metatranscriptomic or total RNA studies generated using NGS short reads. Used for classification of these reads using assembled contigs to reference databases. | workflow, functionally, classify, mRNA, metatranscriptomic, RNA, next, generation, sequencing, NGS, short, read, assembly, contig, reference, database, bio.tools |
is listed by: bio.tools is listed by: Debian |
h2020 EU MicroArctic ITN | Free, Available for download, Freely available | biotools:comw | https://bio.tools/CoMW | SCR_017109 | SciCrunch Registry | 2026-10-17 01:29:14 | 3 | ||||||
|
Scanco: Medical microCT 100 system Resource Report Resource Website 1+ mentions |
Scanco: Medical microCT 100 system (RRID:SCR_017119) | instrument resource | Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG. | SCANCO, micro, CT, computed, tomography, scanner, 3D, imaging, speciment, in vitro, analysis, visualization, image, data | Available for purchase | https://www.scanco.ch/images/Brochures/microct-v16.pdf | http://www.scanco.ch/en/systems-solutions/specimen/microct100.html | SCR_017119 | SciCrunch Registry | 2026-10-17 01:29:39 | 7 | |||||||||
|
Empenn Resource Report Resource Website |
Empenn (RRID:SCR_017074) | community building portal, data or information resource, disease-related portal, portal, project portal, topical portal | Project between Inria, Inserm, CNRS, and University of Rennes for biomedical image analysis for understanding neurological disease. Used to diagnose, monitor and deliver treatment for mental, neurological and substance use disorders by establishing multidisciplinary team between information sciences and medicine in medical imaging, neuroinformatics and population cohorts. | biomedical, image, analysis, disease, medical, imaging, neuroinformatics, population, cohort, brain, neurological, disorder |
is related to: Anima scripts is related to: VISAGES Research is related to: University of Rennes 1; Rennes; France is related to: Anima |
SCR_017074 | SciCrunch Registry | Brain | 2026-10-17 01:29:38 | 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
