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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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cytoNet Resource Report Resource Website |
cytoNet (RRID:SCR_017465) | analysis service resource, data processing software, image analysis software, production service resource, service resource, software application, software resource | Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory. | Cell, population, microscopy, image, network, analysis, quantify, structure, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1533708 | Free, Freely available | SCR_017465 | 2026-08-29 11:25:41 | 0 | |||||||||
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Analysis, Visualization, and Informatics Lab-space (AnVIL) Resource Report Resource Website 10+ mentions |
Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) | AnVIL | data or information resource, data repository, portal, project portal, service resource, storage service resource | Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces. | Dataset, NHGRI, program, NIH, initiative, funded, human, genomic, data, access, sharing, FAIR, analysis, workflow |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
NIH | Restricted | https://www.genome.gov/Funded-Programs-Projects/Computational-Genomics-and-Data-Science-Program/Genomic-Analysis-Visualization-Informatics-Lab-space-AnVIL | SCR_017469 | Visualization, and Informatics Lab-space, AnVIL, Analysis Visualization and Informatics Lab-space, Analysis | 2026-08-29 11:25:41 | 31 | ||||||
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LAN toolbox Resource Report Resource Website 1+ mentions |
LAN toolbox (RRID:SCR_017629) | LANtoolbox | 1d time-series analysis software, data analysis software, data processing software, software application, software resource, software toolkit, time-series analysis software | Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB. | Neuroscientist, data, EEG, experimental, analysis, code, script | is related to: MATLAB | Free, Available for download, Freely available | SCR_017629 | Laboratory of Analysis in Neurosciences Toolbox, EEG Toolbox | 2026-08-29 11:25:47 | 2 | ||||||||
|
Mediation Analysis of Causality under Confounding Resource Report Resource Website |
Mediation Analysis of Causality under Confounding (RRID:SCR_017442) | MACC | data analysis software, data processing software, software application, software resource | Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method. | Casual, mediation, analysis, confounding, correlated, error, data, hierarchical, structure, parameter, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: CRAN |
NIBIB EB022911 | Free, Available for downloads, Freely available | SCR_017442 | Mediation Analysis of Causality under Confounding, macc | 2026-08-29 11:26:00 | 0 | |||||||
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shinyGEO Resource Report Resource Website |
shinyGEO (RRID:SCR_017605) | analysis service resource, production service resource, service resource, software resource, web application | Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets. | Gene, expression, dataset, GEO, differencial, analysis, gene, graphic, omnibus, data, bio.tools |
uses: Shiny is listed by: Debian is listed by: bio.tools has parent organization: Eastern Connecticut State University; Connecticut; United States works with: Gene Expression Omnibus (GEO) |
Google Summer of Code | PMID:27503226 | Free, Available for download, Freely available | biotools:shinygeo | https://gdancik.github.io/shinyGEO/, https://bio.tools/shinygeo | SCR_017605 | 2026-08-29 11:25:46 | 0 | ||||||
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Seizure-Waves Resource Report Resource Website |
Seizure-Waves (RRID:SCR_017455) | data analysis software, data processing software, software application, software resource | Analysis and modeling code for waves of seizure activity. | Analysis, modeling, wave, seizure, brain, activity, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1451384 | Free, Freely available | SCR_017455 | SeizureWaves, Seizure Waves, Seizure-Waves | 2026-08-29 11:25:40 | 0 | ||||||||
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mysamplesize Resource Report Resource Website 1+ mentions |
mysamplesize (RRID:SCR_017575) | data analysis software, data or information resource, data processing software, data visualization software, portal, service resource, software application, software resource | Software tool for experimental design, sample size determination and analysis by Tempest Technologies. | Experimental, design, sample, size, determination, analysis, Tempest Technologies |
is affiliated with: University of California at San Diego; California; USA is affiliated with: University of California at Davis; California; USA |
Restricted | SCR_017575 | MySampleSize | 2026-08-29 11:25:44 | 1 | |||||||||
|
refgenie Resource Report Resource Website 1+ mentions |
refgenie (RRID:SCR_017574) | data management software, service resource, software application, software resource | Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis. | Organize, retrive, share, genome, analysis, reference, assembly, asset, manager, sequence, annotation, file, command, line, interface, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/698704 | Free, Available for download, Freely available | biotools:Refgenie | https://bio.tools/Refgenie | SCR_017574 | reference genome manager | 2026-08-29 11:25:44 | 7 | ||||||
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PoloPlus USB Drive software Resource Report Resource Website 10+ mentions |
PoloPlus USB Drive software (RRID:SCR_017614) | data analysis software, data processing software, software application, software resource | Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB. | LeOra Software LLC, grouped, data, analysis, USB, drive, probit, logit | Restricted | SCR_017614 | Probit Or LOgit Plus USB Drive, PoloPlus USB Drive | 2026-08-29 11:26:01 | 35 | ||||||||||
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StatPackets Resource Report Resource Website |
StatPackets (RRID:SCR_017613) | data or information resource, narrative resource, standard specification | Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together. | Standardized, method, export, statistical, data, KOMP, result, analysis, together | is related to: Knockout Mouse Project | Free, Freely available | SCR_017613 | 2026-08-29 11:25:37 | 0 | ||||||||||
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rjags Resource Report Resource Website 10+ mentions |
rjags (RRID:SCR_017573) | data analysis software, data processing software, software application, software resource | Software package provides interface from R to JAGS library for Bayesian data analysis. Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. | Analysis, Bayesian, hierarchical, model, Markov Chain Monte Carlo, simulation |
is listed by: CRAN is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | https://github.com/cran/rjags/blob/master/INSTALL | SCR_017573 | RJAGS library | 2026-08-29 11:25:36 | 23 | ||||||||
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Dynamo Resource Report Resource Website 1+ mentions |
Dynamo (RRID:SCR_017541) | 3d visualization software, data analysis software, data processing software, data visualization software, image analysis software, image reconstruction software, software application, software resource, time-series analysis software | Software tool for neuron timelapse reconstruction, registration and analysis for Dynamic Morphometrics. | Neuron, dynamic, morphometrics, timelapse, reconstruction, analysis, image | CIHR | Free, Available for download, Freely available | https://padster.github.io/pyDynamo/ | SCR_017541 | pyDynamo, python Dynamo | 2026-08-29 11:26:00 | 2 | ||||||||
|
Transcriptive Resource Report Resource Website |
Transcriptive (RRID:SCR_017545) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results. | Analysis, pipeline, RNA, sequencing, data, raw, FastQ, input, align, read, gene, transcript, count, quality, control | Free, Available for download, Freely available | SCR_017545 | 2026-08-29 11:25:43 | 0 | |||||||||||
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Molecular Devices: Molecular Dynamics Storm 860 Molecular Imager Resource Report Resource Website |
Molecular Devices: Molecular Dynamics Storm 860 Molecular Imager (RRID:SCR_018032) | instrument resource | Multifunction phosphoimager fluorimager laser scanner that collects fluorescent or storage phosphor images from gels, membranes and phosphor screens. It is equipped with blue (450 nm) and red (635 nm) lasers, can scan at resolutions down to 50 microns. It is able to quantify radioactive gels for commonly used isotopes such as 32P, 33P, 125I, 35S, and 14C. There are three detection modes: phosphor screen mode, red/blue fluorescence, chemifluorescence. | ABRF, molecular imager, GE HealthCare, gel, blot, analysis, laser scanner, instrument, equipment | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018032.pdf | Model_Number_Storm 860 Imager | https://btiscience.org/wp-content/uploads/2014/04/Storm_User_Manual.pdf | https://www.mbl.edu/jbpc/files/2014/05/Storm_Info.pdf | SCR_018032 | Storm 860 Molecular Imager, Storm Gel and Blot Imaging System | 2026-08-29 11:25:53 | 0 | ||||||
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GE: Phoenix Nanotom S Resource Report Resource Website 1+ mentions |
GE: Phoenix Nanotom S (RRID:SCR_017995) | instrument resource | System for scientific and industrial nanofocus computed tomography nanoCT and 3D metrology. Realizes unique spatial and contrast resolution on wide sample and application range. Used in material science, precision injection moulding, micromechanics, electronics geology and biology. Used in 3D CT applications. Allows many analysis, e.g. non-destructive visualization of slices, arbitrary sectional views, or automatic pore analysis. | NanoCT, 3D, 3D CT application, spatial, contrast resolution, analysis, non-destructive visualization, slice, section, pore analysis, nanofocus computed tomography | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_017995.pdf | https://www.rcon-ndt.com/products/radiography/x-ray-systems/phoenix-nanotom-s/ | SCR_017995 | 2026-08-29 11:25:51 | 1 | |||||||||
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TCGAbiolinks Resource Report Resource Website 100+ mentions |
TCGAbiolinks (RRID:SCR_017683) | data analysis software, data processing software, software application, software resource | Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R. | Integrative, analysis, TCGA data, cancer, genome, atlas, genomic, analysis, expression, methylated, region, survival plot, phenotype, tumor, epigenomic, alteration, clinical, molecular, retrival | BridgeIRIS ; GENGISCAN ; INNOVIRIS ; Region de Bruxelles Capitale ; Brussels ; Belgium ; São Paulo Research Foundation |
PMID:26704973 DOI:10.12688/f1000research.8923.2 |
Free, Available for download, Freely available | https://github.com/BioinformaticsFMRP/TCGAbiolinks | SCR_017683 | Cancer Genome Atlas (TCGA) biolinks | 2026-08-29 11:25:38 | 112 | |||||||
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Worm Lab Resource Report Resource Website 1+ mentions |
Worm Lab (RRID:SCR_017669) | data analysis software, data processing software, software application, software resource | Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays. | MBF Bioscience, imaging, tracking, analysis, C.elegans, nematode, collect, data, worm, omega, bend, coiling, reversal, entanglement, locomotry, behavior, crawling, swimming, assay | Restricted | SCR_017669 | 2026-08-29 11:25:48 | 8 | |||||||||||
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MOON Resource Report Resource Website 1+ mentions |
MOON (RRID:SCR_018005) | data analysis software, data processing software, software application, software resource, software toolkit | Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid. | Diagnosis, rare disease, next generation sequencing, NGS, data, artificial intelligence, analysis, Diploid | Restricted | SCR_018005 | 2026-08-29 11:25:51 | 6 | |||||||||||
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Vesselucida Explorer Resource Report Resource Website 1+ mentions |
Vesselucida Explorer (RRID:SCR_017674) | data analysis software, data processing software, software application, software resource | Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more. | MBF Bioscience, analysis, vasculature, specific, metric, segment, node, count, frequency, anastomoses, vessel, surface, volume | works with: Vesselucida 360 | Restricted | SCR_017674 | 2026-08-29 11:25:38 | 2 | ||||||||||
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Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | analysis service resource, data analysis service, data management software, production service resource, service resource, software application, software resource | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | 2026-08-29 11:25:17 | 2 |
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