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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Signal Resource Report Resource Website 10+ mentions |
Signal (RRID:SCR_017081) | data acquisition software, data analysis software, data processing software, software application, software resource | Software package for sweep based data acquisition and analysis of time based waveform data obtained through CED digital analogue converter by Cambridge Electronic Design System Limited. Used for transient capture, patch and voltage clamp, LTP studies, evoked response and TMS. | sweep, based, data, acquisition, analysis, time, based, waveform, data, CED, transient, capture, patch, voltage, clamp, LTP study, evoked, response | Available for purchase | SCR_017081 | Signal Version 6, CED Signal, Cambridge Electronic Design Signal | 2026-09-12 12:58:48 | 13 | ||||||||||
|
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 | rCASC, reproducible Cluster Analysis of Single Cells | 2026-09-12 12:58:47 | 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 | , International Neuroinformatics Coordinating Facility Neurobot, INCF Neurobot | 2026-09-12 12:58:47 | 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 | 2026-09-12 12:58:48 | 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 | 2026-09-12 12:58:47 | 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 | Cytometry dATa anALYSis Tools | 2026-09-12 12:58:48 | 241 | |||||
|
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 | 2026-09-12 12:58:48 | 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 | 2026-09-12 12:58:47 | 324 | |||||||
|
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 | The Lipid Ontology (LION), Lipid Ontology, LIpid ONtology (LION), LIpid ONtology, LION | 2026-09-12 12:58:47 | 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 | 2026-09-12 12:58:47 | 20 | |||||||||
|
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 | Generally Applicable Gene-set Enrichment for pathway analysis, gage, Generally Applicable Gene-set Enrichment, GSEA | 2026-09-12 12:58:48 | 53 | |||||||||
|
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 | 2026-09-12 12:58:48 | 7 | |||||||||
|
Source code for analysis of GC-MS data - Rice HxD Project Resource Report Resource Website 1+ mentions |
Source code for analysis of GC-MS data - Rice HxD Project (RRID:SCR_017073) | data analysis software, data processing software, data visualization software, software application, software resource, source code | Source code used in the analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice exposed to combined drought and heat stress. | analysis, GC-MS, data, rice, sample, statistics, workflow | Free, Available for download, Freely available | SCR_017073 | 2026-09-12 12:58:48 | 1 | |||||||||||
|
affydata Resource Report Resource Website |
affydata (RRID:SCR_016976) | AffyData | data analysis software, data or information resource, data processing software, software application, software resource | Software R package for analysis of Affymetrix Data. Contains samples data files of a large size. | analysis, Affymetrix, data, large, dataset, oligonucleotide, array |
is listed by: Bioconductor is related to: affy is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016976 | affydata, Affymetrix Data, Affymetrix Data for Demonstration Purpose | 2026-09-12 12:58:46 | 0 | ||||||||
|
Heatmapper Resource Report Resource Website 100+ mentions |
Heatmapper (RRID:SCR_016974) | data access protocol, data processing software, software application, software resource, web service | Software tool to create and provide heat maps through a graphical interface. Allows to create an expression, pairwise comparison, image overlay, geomap, and geocoordinate heat maps for different data types and applications. Used to interactively visualize data. | expression, based, heat, map, pairwise, comparison, distance, correlation, image, overlay, latitude, longitude, geomap, geopolitical, geocoordinate, choropleth, data, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing has parent organization: Wishart Research Group is provided by: University of Alberta; Alberta; Canada |
Canadian Institutes of Health Research ; Genome Alberta |
PMID:27190236 | Freely available, Free, Acknowledgement requested | OMICS_12077, biotools:heatmapper | http://www.heatmapper.ca, https://github.com/WishartLab/heatmapper, https://bio.tools/heatmapper | SCR_016974 | Heatmapper, HeatMapper, heat mapper | 2026-09-12 12:58:46 | 252 | |||||
|
Collaborative Computing Project for NMR Resource Report Resource Website 10+ mentions |
Collaborative Computing Project for NMR (RRID:SCR_016983) | CCPN | data or information resource, discussion, forum, narrative resource, portal, project portal | Project provides tools and knowledge to maximize the impact of the biological NMR studies. CCPN software facilitates data analysis and software integration. Project promotes the exchange of knowledge and provides training and best practices for the NMR community and has leading role in the development of NMR data sharing standard and coordination of NMR instrumentation proposals. Includes CCPN Data Model for macromolecular NMR and related areas, CcpNmr suite of programs like Analysis for spectrum visualization, resonance assignment and analysis, ChemBuild to create chemical structure templates in an NMR aware manner, FormatConverter for data exchange with common textual NMR formats and SpecView for swift, format independent peak and spectrum visualization. | collaborative, computing, project, NMR, software, data, standard, protein, molecule, spectroscopy, global |
is related to: University of Leicester; Leicester; United Kingdom is related to: CCPN Analysis is parent organization of: CCPN Data Model |
Astra-Zeneca ; BBSRC ; Dupont Pharma ; Genentech ; GlaxoSmithKline ; Medical Research Council |
PMID:15613391 | Free for non profit, Public, Acknowledgement requested | https://sourceforge.net/projects/ccpn/ | SCR_016983 | CCPN, Collaborative Computing Project for NMR, The Collaborative Computing Project for NMR | 2026-09-12 12:58:46 | 23 | |||||
|
BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | data analysis software, data processing software, software application, software resource | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NCRR P20 RR01 6460; NIGMS P20 GM103429; NSF 1553680 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download, http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download, https://bio.tools/binpacker | SCR_017038 | 2026-09-12 12:58:47 | 10 | ||||||
|
CCPN Data Model Resource Report Resource Website |
CCPN Data Model (RRID:SCR_016982) | data or information resource, data processing software, data repository, data storage software, database, service resource, software application, software resource, storage service resource | Model to cover data for macromolecular NMR spectroscopy from the initial experimental data to the final validation. Used for the large scale data deposition, data mining and program interoperability. Enables movement from one software package to another without difficulties with data conversion or loss of information. Works with CcpNmr Analysis software for analysis and interactive display, CcpNmr FormatConverter for allowing transfer of data from programs used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment. Used within the CCPN software suite for NMR spectroscopy and at the BioMagResBank for converting existing deposited restraint lists to a standard IUPAC nomenclature. | data, macromolecular, NMR, spectroscopy, deposition, mining, interoperability, conversion |
is related to: Biological Magnetic Resonance Data Bank (BMRB) has parent organization: Collaborative Computing Project for NMR works with: CCPN Analysis works with: CCPN Analysis |
BBSRC ; EU ; NIGMS GM67965; NLM P41 LM005799 |
PMID:15815974 PMID:15613391 PMID:21953355 |
Free, Public | SCR_016982 | The CCPN Data Model | 2026-09-12 12:58:46 | 0 | |||||||
|
CCPN Analysis Resource Report Resource Website 10+ mentions |
CCPN Analysis (RRID:SCR_016984) | CcpNmr Analysis | data analysis software, data processing software, data visualization software, software application, software resource | Software package for interactive NMR spectrum visualization, resonance assignment and data analysis. Graphical elements allow to enter information and to view status of data and library functions manipulate the CCPN data model objects to record the scientific information. Software is cross platform and works on Linux, Mac OSX, Windows and Unix. | interactive, NMR, specturm, visualization, resonance, data, analysis |
is related to: University of Cambridge; Cambridge; United Kingdom is related to: Python Programming Language is related to: Collaborative Computing Project for NMR works with: CCPN Data Model works with: CCPN Data Model |
Biotechnology and Biological Sciences Research Council (UK) ; Deutsche Forschungsgemeinschaft |
PMID:21953355 PMID:15815974 |
Public, Available for download, Free of charge for non profit institutions, Tutorial available | SCR_016984 | CcpNmr Analysis, CCPN Analysis v2, CCPN Analysis v3 | 2026-09-12 12:58:46 | 48 | ||||||
|
Digital Access to Scholarship at Harvard Resource Report Resource Website |
Digital Access to Scholarship at Harvard (RRID:SCR_004122) | DASH | data or information resource, data repository, database, service resource, storage service resource | Harvard University''s central service for sharing and preserving work. In addition to the scholarly journal articles targeted by Harvard''s several open access resolutions, DASH maybe used to self-archive manuscripts and materials. DASH supports a variety of file formats, and users are encouraged to deposit related materials with manuscripts (including data, images, audio and video files, etc.) When users deposit their work in DASH, it becomes visible to colleagues around the world by virtue of metadata harvesting, Google Scholar, and other indexing services. Higher visibility leads to higher rates of citation and impact. When users post early versions of their work, before publication, they establish intellectual priority sooner. Users act in their own best interests by taking part in the University''s mission to share and preserve the knowledge produced there. Because Harvard now has a prior, non-exclusive license to faculty journal articles in schools with open access policies, those faculty members are required to act accordingly when publishing journal articles, either by attaching an addendum to their publication agreement or obtaining a waiver. They then must deposit the publication in DASH. | scholarship, image, audio clip, video resource, manuscript, data | has parent organization: Harvard University; Cambridge; United States | nlx_158606 | SCR_004122 | 2026-09-12 12:56:09 | 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
