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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Mouse Behavioral Analysis Toolbox Resource Report Resource Website 1+ mentions |
Mouse Behavioral Analysis Toolbox (RRID:SCR_023291) | MouBeAT | software toolkit, software resource | Software package to analyze different behavioral tests in rodents semi-automatically. These tests include Open Field (OF), Elevated Plus Maze (EPM), Y-maze (YM) test and Morris Water Maze (MWM). | OpenBehavior, behavioral tests, behavioral tests analysis, tests in rodents |
uses: ImageJ is listed by: OpenBehavior |
Ministry of Science and Innovation ; Spain ; European Regional Development Fund |
PMID:30245618 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/moubeat/ | SCR_023291 | 2026-08-09 09:08:35 | 1 | ||||||
|
vcfR Resource Report Resource Website 1+ mentions |
vcfR (RRID:SCR_023453) | software toolkit, software resource | Software R package to read, write, manipulate and analyze variant call format data. Facilitates easy manipulation of variant call format (VCF) data. | Manipulate and visualize VCF data, variant call format data, VCF data, extract data matrices, genomic data visualization, VCF file, variant call format files, | is listed by: CRAN | Free, Available for download, Freely available | https://knausb.github.io/vcfR_documentation/, https://github.com/knausb/vcfR, https://cran.r-project.org/web/packages/vcfR/vignettes/intro_to_vcfR.html, | SCR_023453 | variant call format in R | 2026-08-09 09:08:36 | 9 | ||||||||
|
poppr Resource Report Resource Website 10+ mentions |
poppr (RRID:SCR_023452) | software toolkit, software resource | Software R package for analysis of populations with mixed modes of sexual and clonal reproduction. Used for genetic analysis of populations with mixed reproduction. | genetic analysis, mixed reproduction, mixed reproduction populations, mixed modes, sexual and clonal reproduction, | US Department of Agriculture ; USDA National Institute of Food and Agriculture ; USDA ARS Floriculture Nursery Initiative ; USDA-Forest Service Forest Health Monitoring Program |
DOI:10.7717/peerj.281 DOI:10.3389/fgene.2015.00208 |
Free, Available for download, Freely available | https://CRAN.R-project.org/package=poppr, https://github.com/grunwaldlab/poppr/ | SCR_023452 | 2026-08-09 09:08:39 | 14 | ||||||||
|
Computing Chance Corrected Agreement Coefficients Resource Report Resource Website 1+ mentions |
Computing Chance Corrected Agreement Coefficients (RRID:SCR_023176) | irrCAC | software toolkit, software resource | Software R package to calculate various chance-corrected agreement coefficients among 2 or more raters. Among CAC coefficients covered are Cohen's kappa, Conger's kappa, Fleiss' kappa, Brennan-Prediger coefficient, Gwet's AC1/AC2 coefficients, and Krippendorff's alpha. Multiple sets of weights are proposed for computing weighted analyses. | CAC coefficients, chance-corrected agreement coefficients calculations, computing weighted analyses | is listed by: CRAN | Free, Available for download, Freely available | SCR_023176 | Computing Chance-Corrected Agreement Coefficients | 2026-08-09 09:08:32 | 2 | ||||||||
|
Intraclass Correlations for Quantifying Inter Rater Reliability Resource Report Resource Website 1+ mentions |
Intraclass Correlations for Quantifying Inter Rater Reliability (RRID:SCR_023175) | irrICC | software toolkit, software resource | Software R package to calculate various intraclass correlation coefficients. Used to quantify inter-rater and intra-rater reliability. | intraclass correlation coefficients calculation, correlation coefficient | is listed by: CRAN | Free, Available for download, Freely available | SCR_023175 | Intraclass Correlations for Quantifying Inter-Rater Reliability | 2026-08-09 09:08:32 | 1 | ||||||||
|
SURVIVOR Resource Report Resource Website 10+ mentions |
SURVIVOR (RRID:SCR_022995) | SURVIVOR | software toolkit, software resource | Software tool set for simulating and evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs. Used for for SV simulation, comparison and filtering. | Structural Variant, simulating and evaluating SVs, merging and comparing SVs, reformat or summarize SVs, | Swiss National Science Foundation ; National Science Foundation DBI-1350041; NHGRI R01-HG006677; Wellcome Trust Senior Investigator Award ; Royal Society Wolfson Research Merit Award ; EPSRC Centre for Doctoral Training studentship at UCL CoMPLEX |
PMID:28117401 | Free, Available for download, Freely available | SCR_022995 | StructURal Variant majorIty VOte | 2026-08-09 09:08:30 | 16 | |||||||
|
Rtrack Resource Report Resource Website |
Rtrack (RRID:SCR_023025) | software toolkit, software resource | Software R package for analysis of paths from spatial tracking experiments such as Morris water maze and calculation of goal finding strategies. Used for in depth analysis of tracking coordinates from video. | OpenBehavior, process raw spatial tracking data, calculate behavioural strategies, spatial tracking experiments, Morris water maze |
is listed by: OpenBehavior is listed by: CRAN |
DOI:10.1101/2020.02.27.967372v1.full.pdf | Free, Available for download, Freely available | https://rupertoverall.net/Rtrack/, https://edspace.american.edu/openbehavior/?s=Rtrack | SCR_023025 | 2026-08-09 09:08:29 | 0 | ||||||||
|
Merqury Resource Report Resource Website 50+ mentions |
Merqury (RRID:SCR_022964) | software toolkit, software resource | Software toolkit for reference free quality, completeness, and phasing assessment for genome assemblies. Genome assembly quality evaluation based on k-mers. | reference free quality, completeness, phasing assessment, genome assemblies, quality evaluation based on k-mers | NHGRI | PMID:32928274 | Free, Available for download, Freely available | SCR_022964 | 2026-08-09 09:08:29 | 72 | |||||||||
|
GetOrganelle Resource Report Resource Website 100+ mentions |
GetOrganelle (RRID:SCR_022963) | software toolkit, software resource | Software toolkit to assembly of organelle genome from genomic skimming data. Used for accurate de novo assembly of organelle genomes. | Organelle genome assembly, genomic skimming data, organelle genomes, de novo assembly | Chinese Academy of Sciences ; National Natural Science Foundation of China |
PMID:32912315 | Free, Available for download, Freely available | SCR_022963 | 2026-08-09 09:08:27 | 256 | |||||||||
|
TBtools Resource Report Resource Website 1000+ mentions |
TBtools (RRID:SCR_023018) | software toolkit, software resource | Software integrative toolkit developed for interactive analyses of big biological data. | interactive analyses, big biological data | Free, Available for download, Freely available | SCR_023018 | Tools for Biologist | 2026-08-09 09:08:30 | 1297 | ||||||||||
|
JupiterPlot Resource Report Resource Website 10+ mentions |
JupiterPlot (RRID:SCR_022961) | software toolkit, software resource | Software pipeline for generating Circos based genome assembly consistency plot given set of contigs relative to reference genome. Intended to visualize large scale translocations or missassemblies in draft assemblies, but it can also be useful when trying to show synteny between whole genomes.Circos based tool to visualize genome assembly consistency | visualize large scale translocations, visualize large scale missassemblies in draft assemblies, visualize genome assembly consistency, consistency plot, set of contigs relative to reference genome, | is related to: Circos | Free, Available for download, Freely available | SCR_022961 | 2026-08-09 09:08:29 | 20 | ||||||||||
|
AmpliconArchitect Resource Report Resource Website 50+ mentions |
AmpliconArchitect (RRID:SCR_023150) | software toolkit, software resource | Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers. | call circular DNA, short read WGS data, connected genomic regions identification, simultaneous copy number amplification, amplicon | NIGMS R01GM114362; NHGRI HG010149; NSF NSF-DBI-1458557 |
DOI:10.1038/s41467-018-08200-y | SCR_023150 | 2026-08-09 09:08:13 | 53 | ||||||||||
|
findCPcli Resource Report Resource Website 1+ mentions |
findCPcli (RRID:SCR_023391) | software toolkit, software resource | Software command line Python package for computation of chokepoint reactions in genome scale metabolic models. Used to compute chokepoints by taking into account both topology and dynamic information of network. Can compute and remove dead-end metabolites, find essential reactions and update flux bounds of reactions according to results of Flux Variability Analysis. | compute chokepoints, chokepoint reactions, genome scale metabolic models, network topology and dynamic information, | DOI:10.1007/978-3-030-60327-4_6 | Free, Available for download, Freely available | https://findcpcli.readthedocs.io/en/latest/ | SCR_023391 | 2026-08-09 09:08:37 | 1 | |||||||||
|
openFPGALoader Resource Report Resource Website |
openFPGALoader (RRID:SCR_023153) | software toolkit, software resource | Universal utility for programming FPGAs. Compatible with many boards, cables and FPGA from major manufacturers (Xilinx, Altera/Intel, Lattice, Gowin, Efinix, Anlogic, Cologne Chip). Works on Linux, Windows and macOS. | Field programmable gate array, FPGA, | Free, Available for download, Freely available | SCR_023153 | 2026-08-09 09:08:13 | 0 | |||||||||||
|
synchCams Resource Report Resource Website 1+ mentions |
synchCams (RRID:SCR_023152) | software toolkit, software resource | Software toolbox for synchronized dual camera acquisition. Library for acquisition of synchronized dual camera video. Videos are saved with alternate acquisition of frames what ensures equal number of frames. | synchronized dual camera acquisition, synchronized dual camera video library, camera acquisition | Free, Available for download, Freely available | SCR_023152 | 2026-08-09 09:08:32 | 2 | |||||||||||
|
Simple Features Resource Report Resource Website 10+ mentions |
Simple Features (RRID:SCR_023393) | sf | software toolkit, software resource | Software R package as set of standards that specify common storage and access model of geographic features made of mostly two dimensional geometries used by geographic information systems. Standardized way to encode spatial vector data. Formalized by Open Geospatial Consortium and International Organization for Standardization. | common storage, access model, geographic features, two dimensional geometries, geographic information systems | is listed by: CRAN | Free, Available for download, Freely available | Also https://r-spatial.github.io/sf/, https://github.com/r-spatial/sf/ | SCR_023393 | Simple Feature Access, simple features | 2026-08-09 09:08:15 | 15 | |||||||
|
iGraph/M Resource Report Resource Website 1+ mentions |
iGraph/M (RRID:SCR_023308) | software toolkit, software resource | Software package for use in complex networks and graph theory research. Mathematica interface for igraph. Provides Mathematica interface to popular igraph network analysis package, as well as many other functions for working with graphs in Mathematica. IGraph/M comes pre-packaged and ready to use on Windows, OS X and Linux (64-bit Intel), as well as the Raspberry Pi computer. The code is open source and can be compiled on other platforms as well (such as 32-bit Windows). | Mathematica interface for igraph, complex networks and graph theory, | Free, Available for download, Freely available | http://szhorvat.net/mathematica/IGDocumentation/ | SCR_023308 | 2026-08-09 09:08:14 | 2 | ||||||||||
|
mtradeR Resource Report Resource Website 1+ mentions |
mtradeR (RRID:SCR_022977) | software toolkit, software resource | Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually. | test association between taxa and disease risk, correlated taxa screening, taxa and disease risk | NIDDK U24DK097771; NCI CA21765; American Lebanese Syrian Associated Charities |
PMID:36123651 | Free, Available for download, Freely available | SCR_022977 | Metagenomic TRajectory Analysis with Disease Endpoint and Risk factors | 2026-08-09 09:08:10 | 1 | ||||||||
|
org.Mm.eg.db Resource Report Resource Website 10+ mentions |
org.Mm.eg.db (RRID:SCR_023488) | software toolkit, software resource | Software package for genome wide annotation for mouse, primarily based on mapping using Entrez Gene identifiers. | genome wide annotation for mouse, mapping using Entrez Gene identifiers, | Free, Available for download, Freely available | SCR_023488 | 2026-08-09 09:08:16 | 12 | |||||||||||
|
SCRuB Resource Report Resource Website 1+ mentions |
SCRuB (RRID:SCR_023518) | software toolkit, software resource | Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program. | Source tracking, contamination removal, microBiomes, MiSeq decontamination, contamination in microbial studies, | Rockefeller University ; Columbia University ; CIFAR Azrieli Global Scholarship ; NICHD R01HD106017; NCI R01CA245894 |
PMID:36928429 | Free, Available for download, Freely available | SCR_023518 | Source-tracking for Contamination Removal in microBiomes, Source tracking for Contamination Removal in microBiomes | 2026-08-09 09:08:16 | 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
