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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Yevis cli Resource Report Resource Website 1+ mentions |
Yevis cli (RRID:SCR_023204) | software application, software resource | Software CLI tool to support building and maintaining Yevis workflow registry. | Yevis workflow registry, Yevis, workflow registry with automated quality control, | is related to: Yevis web | Free, Available for download, Freely available | https://sapporo-wes.github.io/yevis-cli/getting_started | SCR_023204 | Yevis-cli | 2026-08-09 09:08:13 | 2 | ||||||||
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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 | ||||||||
|
HOMA2 calculator Resource Report Resource Website 50+ mentions |
HOMA2 calculator (RRID:SCR_023419) | software application, software resource | Software tool used to calculate Homeostasis Model Assessment which takes account of variations in hepatic and peripheral glucose resistance, increases in insulin secretion curve for plasma glucose concentrations and contribution of circulating proinsulin. Provides access to HOMA2 model for researchers who wish to use model derived estimates of %B and %S, rather than linear approximations. | calculate Homeostasis Model Assessment, Homeostasis Model Assessment, HOMA calculator | is related to: iHOMA2 | Free, Available for download, Freely available | SCR_023419 | HOMA Calculator | 2026-08-09 09:08:38 | 81 | |||||||||
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Vitrea Read Diagnostic Viewer Resource Report Resource Website 1+ mentions |
Vitrea Read Diagnostic Viewer (RRID:SCR_023418) | software application, software resource | Software application providing tools and features that may be used for general purpose radiological viewing and reading of image data from various imaging modalities, clinical review and performs functions of digital image processing, measurement, communications and storage. | Canon Medical Informatics, Inc., Diagnostic Viewer, radiological image viewing and reading, image data, digital image processing, | Restricted | https://www.vitalimages.com/enterprise-imaging-solution/enterprise-viewer/ | SCR_023418 | Diagnostic Viewer, Vitrea EasyViz Diagnostic Viewer, Vitrea Read, Vitrea EasyViz | 2026-08-09 09:08:15 | 1 | |||||||||
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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 | ||||||||||
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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 | ||||||||||
|
SAMI Ex Resource Report Resource Website |
SAMI Ex (RRID:SCR_023271) | software application, software resource | Software tool provides automation and process control across wide variety of applications, creates planned data driven schedules in optimized and predictable scheduling environment. | Beckman Coulter, Life Sciencies, automation and process control, planned data driven schedules, scheduling environment | Restricted | SCR_023271 | 2026-08-09 09:08:34 | 0 | |||||||||||
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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 | |||||||||
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mitochondria simulator Resource Report Resource Website 1+ mentions |
mitochondria simulator (RRID:SCR_023430) | software application, software resource | Software repository for mtDNA assembly project. | mitochondria, assembly, de bruijn graph, data mining, mtDNA assembly project, | Free, Available for download, Freely available | SCR_023430 | mitochondria-simulator | 2026-08-09 09:08:36 | 8 | ||||||||||
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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 | |||||||||||
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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 | |||||||||||
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Data Acquisition and Reporting Tool Resource Report Resource Website |
Data Acquisition and Reporting Tool (RRID:SCR_023272) | DART | software application, software resource | Software package that gathers data and synthesizes runtime information from Biomek log files to capture each manipulation of sample during course of method. | Beckman Coulter, Life Sciences, Biomek log files, capture each sample manipulation, gathers data and synthesizes runtime information, | Restricted | SCR_023272 | 2026-08-09 09:08:33 | 0 | ||||||||||
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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 | |||||||
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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 | ||||||||||
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RepFinder Resource Report Resource Website |
RepFinder (RRID:SCR_023429) | software application, software resource | Software tool to find shared repeats between mitochondrial genomes. | mitochondrion, mtDNA, find shared repeats, mitochondrial genomes, | Free, Available for download, Freely available | SCR_023429 | 2026-08-09 09:08:38 | 0 | |||||||||||
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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 | ||||||||
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OmicsGAN Resource Report Resource Website 1+ mentions |
OmicsGAN (RRID:SCR_022976) | software application, software resource | Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals. | integrate two omics data, interaction network, generate one synthetic data corresponding to each omics profile, phenotype prediction | NSF III1755761; NIGMS R01GM113952; NIDA DK097771 |
PMID:34415323 | Free, Available for download, Freely available | SCR_022976 | Omics Generative Adversarial Network | 2026-08-09 09:08:29 | 1 |
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