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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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UCL Medical School; London; United Kingdom Resource Report Resource Website |
UCL Medical School; London; United Kingdom (RRID:SCR_002211) | university | Medical school at the University College London that provides undergraduate and postgraduate medical education programs, educational research, and specializations in variety of medical subfields. | medical school, london, medical education research |
has parent organization: University College London; London; United Kingdom is parent organization of: UCL-RFH BioBank |
Free | nlx_143837 | SCR_002211 | University College London Medical School, UCL Medical School | 2026-07-25 12:05:18 | 0 | ||||||||
|
Genoscope Resource Report Resource Website 100+ mentions |
Genoscope (RRID:SCR_002172) | Genoscope | institution | French national sequencing center with the following resources: * Sequencing ** Genoscope Projects * Environmental genomics ** Microbial diversity in wastewater ** Metabolic genomics * Bioinformatics ** Atelier for comparative genomics ** Computational Systems Biology ** Servers resources *** GGB for Generic Genome Browser: graphic interface for various databases (sequence, annotation, syntenies...) for a given organism. *** MaGe for Magnifying Microbial Genomes: annotation system for microbial genomes. | environmental genomics, biocatalysis, environment, genomics, sequencing, bioinformatics, biodiversity, blast, blat, ggb, mage, metabolic, whole genome shotgun, chromosome 3, cdna, chromosome 14, alternative splicing, o��kopleura dioica, mutation, enzymatic cloning, screening, synteny, data set, genome, sequence, annotation, genome browser, FASEB list | has parent organization: CEA; Gif sur Yvette; France | Free, Freely available | ISNI: 0000 0004 0641 2997, Wikidata: Q3100800, grid.434728.e, nif-0000-20957 | https://ror.org/028pnqf58 | SCR_002172 | Genoscope - Centre National de S�quen�age, Genoscope - French National Sequencing Center, French National Sequencing Center, Genoscope - Centre National de Sequencage | 2026-07-25 12:05:17 | 158 | ||||||
|
DEMI Resource Report Resource Website 1+ mentions |
DEMI (RRID:SCR_002291) | software resource | R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes. | standalone software, affymetrix, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24586062 | Free, Available for download, Freely available, Acknowledgement requested | OMICS_03438 | http://cran.r-project.org/web/packages/demi/ | SCR_002291 | demi: Differential Expression from Multiple Indicators, Differential Expression from Multiple Indicators | 2026-07-25 12:05:23 | 6 | ||||||
|
flowCore Resource Report Resource Website 100+ mentions |
flowCore (RRID:SCR_002205) | software resource | A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is used by: flowBeads is listed by: OMICtools has parent organization: Bioconductor |
PMID:19358741 | Artistic License, v2 | OMICS_05596 | SCR_002205 | flowCore: Basic structures for flow cytometry data | 2026-07-25 12:05:21 | 350 | |||||||
|
CIGAL Resource Report Resource Website 1+ mentions |
CIGAL (RRID:SCR_002232) | CIGAL | software resource | Software program that provides accurate real-time stimulus control, behavioral and physiological recording, and synchronization with external devices. It can also provide continuous real-time feedback of task performance and physiological responses. Task programming typically involves a simple text file specifying basic parameter settings (e.g. screen color) and a list of stimulus events, which can include images, animated movies, sound files, text stimuli, video graphics, or commands that communicate with external hardware devices. Multiple video and auditory stimuli can be presented simultaneously. Multi-channel response recording and real-time feedback features require no user programming. Advanced users can add customized stimulus events using CIGAL's real-time programming capabilities. Output files can be automatically created in a variety of output formats (e.g. FSL 3-column files, XML Events files, CSV trial tables). | magnetic resonance, stimulus control, behavioral recording, physiological recording |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Duke University; North Carolina; USA |
Free, Available for download, Freely available | nlx_155528 | http://www.nitrc.org/projects/cigal | http://fourier.biac.duke.edu/wiki/doku.php/jvs:cigal | SCR_002232 | Compilable Imaging Graphics and Analytical Language | 2026-07-25 12:05:19 | 6 | |||||
|
NIfTImatlab Resource Report Resource Website 1+ mentions |
NIfTImatlab (RRID:SCR_002230) | NIfTImatlab | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28, 2025. Software tool that allows the user to operate on NIfTI image files from Matlab. | matlab, nifti, image | has parent organization: New York University; New York; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155526 | SCR_002230 | NYU CBI NIfTI Matlab tool | 2026-07-25 12:05:18 | 1 | |||||||
|
4D Atlases Construction Resource Report Resource Website 1+ mentions |
4D Atlases Construction (RRID:SCR_002227) | software resource | Software package for constructing longitudinal atlases, which are the necessary steps for many brain-related applications. | magnetic resonance, altas, brain, software package |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
PMID:34891818 PMID:31115143 |
Free, Available for download, Freely available | nlx_155688 | http://www.nitrc.org/projects/atlas4d | http://www.med.unc.edu/bric/ideagroup/free-softwares/4d-atlases-construction | SCR_002227 | 4D Atlas Construction Toolbox, 4D Atlas Construction | 2026-07-25 12:05:18 | 1 | |||||
|
University of Amsterdam; Amsterdam; Netherlands Resource Report Resource Website |
University of Amsterdam; Amsterdam; Netherlands (RRID:SCR_002385) | UvA | university | Public research university in the Netherlands that offers programs in humanities, social and behavioural sciences, economics and business, science, law, medicine, and dentistry. | netherlands public university, public university, netherlands research, degree program |
is affiliated with: OpenMinTeD is parent organization of: A modular structure for scientific articles in an electronic environment is parent organization of: X-linked Adrenoleukodystrophy Database is parent organization of: T-profiler is parent organization of: 7T Structural MRI scans ATAG is parent organization of: ENVRI-KMS is parent organization of: R2 Genomics Analysis and Visualization Platform |
nlx_19684 | SCR_002385 | University of Amsterdam, Universiteit van Amsterdam | 2026-07-25 12:05:25 | 0 | ||||||||
|
flowBeads Resource Report Resource Website |
flowBeads (RRID:SCR_002440) | software resource | Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
uses: flowCore is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available | OMICS_05592 | SCR_002440 | flowBeads: Analysis of flow bead data | 2026-07-25 12:05:22 | 0 | ||||||||
|
Multi-Modal MRI Reproducibility Resource Resource Report Resource Website 10+ mentions |
Multi-Modal MRI Reproducibility Resource (RRID:SCR_002442) | Multi-Modal MRI Reproducibility Resource | image collection, data or information resource | Scan-rescan imaging sessions on 21 healthy volunteers (no history of neurological disease) intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic 1 hour session at 3T. Imaging modalities include MPRAGE, FLAIR, DTI, resting state fMRI, B0 and B1 field maps, ASL, VASO, quantitative T1 mapping, quantitative T2 mapping, and magnetization transfer imaging. All data have been converted to NIFTI format. Please cite: Bennett. A. Landman, Alan J. Huang, Aliya Gifford, Deepti S. Vikram, Issel Anne L. Lim, Jonathan A.D. Farrell, John A. Bogovic, Jun Hua, Min Chen, Samson Jarso, Seth A. Smith, Suresh Joel, Susumu Mori, James J. Pekar, Peter B. Barker, Jerry L. Prince, and Peter C.M. van Zijl. ?Multi-Parametric Neuroimaging Reproducibility: A 3T Resource Study?, NeuroImage. (2010) NIHMS/PMC:252138 doi:10.1016/j.neuroimage.2010.11.047 | java image science toolkit, magnetic resonance, nifti, neuroimaging, reproducibility, mprage, flair, dti, resting state fmri, b0 field map, b1 field map, asl, vaso, quantitative t1 mapping, quantitative t2 mapping, magnetization transfer imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit |
Healthy | PMID:21094686 | Free, Available for download, Freely available | nlx_155818 | SCR_002442 | 2026-07-25 12:05:26 | 11 | ||||||
|
Cogprints: Cognitive Sciences EPrint Archive Resource Report Resource Website 1+ mentions |
Cogprints: Cognitive Sciences EPrint Archive (RRID:SCR_002314) | journal article | An electronic archive for self-archive papers in any area of Psychology, neuroscience, and Linguistics, and many areas of Computer Science, Philosophy, Biology, Medicine, Anthropology, cognitive ethnology, archeology, paleontology, as well as any other portions of the physical, social and mathematical sciences that are pertinent to the study of cognition. | ethnology, anthropology, archeology, biology, cognition, cognitive science, computer science, linguistics, mathematical, medicine, neuroscience, paleontology, philosophy, physical, psychology, science, scientific literature databases and services, social | has parent organization: University of Southampton; Southampton; United Kingdom | nif-0000-21093 | SCR_002314 | Cogprints | 2026-07-25 12:05:20 | 3 | |||||||||
|
flowCyBar Resource Report Resource Website 1+ mentions |
flowCyBar (RRID:SCR_002319) | software resource | A software package to analyze flow cytometric data using gate information to follow population / community dynamics. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 | OMICS_05597 | SCR_002319 | flowCyBar - Analyze flow cytometric data using gate information | 2026-07-25 12:05:20 | 5 | ||||||||
|
Confocal Microscopy Image Gallery - Rat Brain Tissue Sections Resource Report Resource Website |
Confocal Microscopy Image Gallery - Rat Brain Tissue Sections (RRID:SCR_002432) | image collection, data or information resource | An image gallery of the rat brain labeled via immunofluorescence in coronal, horizontal, and sagittal thick sections using laser scanning confocal microscopy. | image collection, gallery, function, amygdala, anatomy, blood vessel, brain, cerebellum, cerebral cortex, coronal, digital image, hippocampus, horizontal, hypothalamus, immunofluorescence, microscopy, model, neuron microscopy, rat, receptor, sagittal, thalamus, tissue | is provided by: Olympus | Free, Freely available | nif-0000-21299 | http://www.olympusconfocal.com/gallery/ratbrain/ | SCR_002432 | Olympus Rat Brain Tissue Sections | 2026-07-25 12:05:26 | 0 | |||||||
|
VS-Lite Resource Report Resource Website 1+ mentions |
VS-Lite (RRID:SCR_002431) | VS-Lite | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. A simple, efficient, process-based forward model of tree-ring growth, requires as inputs only latitude and monthly temperature and precipitation. | model, mathematical model, tree ring, dendrochronology, tree ring width, tree, ring, ring growth model |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
NOAA ; NSF 0724802 |
THIS RESOURCE IS NO LONGER IN SERVICE. | SciRes_000128 | SCR_002431 | Vaganov-Shashkin-Lite, Vaganov-Shashkin-Lite Model of Tree-Ring Width | 2026-07-25 12:05:22 | 2 | ||||||
|
ANOVA Resource Report Resource Website 100+ mentions |
ANOVA (RRID:SCR_002427) | ANOVA | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. Matlab code for two-factor (location and year) analysis-of-variance model for the calculation of climate anomalies, in which the reference interval is specified as the full length of the dataset. This scheme avoids the affects of shorter (e.g. 1961-1990) reference intervals on the temporal evolution of the spatial standard deviation of climate anomalies. Data files provided. | model program, anomaly, anomaly, climate, variance, climate anomaly, matlab |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
PMID:27406694 PMID:15866832 |
THIS RESOURCE IS NO LONGER IN SERVICE. | SciRes_000129 | SCR_002427 | Analysis of Variance | 2026-07-25 12:05:22 | 343 | ||||||
|
DWGSIM Resource Report Resource Website 50+ mentions |
DWGSIM (RRID:SCR_002342) | DWGSIM | software resource | Whole Genome Simulator for Next-Generation Sequencing. | next-generation sequencing, whole genome simulation |
is listed by: OMICtools is listed by: Debian |
GNU General Public License, v2 | OMICS_00249 | https://sources.debian.org/src/dwgsim/ | SCR_002342 | 2026-07-25 12:05:20 | 51 | |||||||
|
BEETL-fastq Resource Report Resource Website |
BEETL-fastq (RRID:SCR_002341) | software resource | Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads. | Searchable compressed archive, DNA reads, compresses FASTQ-formatted DNA reads, bio.tools, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Burrows-Wheeler transform |
PMID:24950811 | Free, Available for download, Freely available | OMICS_04900, biotools:beetl | https://bio.tools/beetl | SCR_002341 | 2026-07-25 12:05:24 | 0 | |||||||
|
HIBAL Resource Report Resource Website |
HIBAL (RRID:SCR_002461) | HIBAL | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. FORTRAN code for a simple hydrologic-isotopic-balance model for application to paleolake d18O records. Inputs to the model include discharge, on-lake precipitation, evaporation, and the d18O values of these fluid fluxes. Benson and Paillet (2002) | d18o, hydrologic isotopic balance model, paleolake, hydrology, hydrologic, isotopic, balance, model, fortran, discharge, evaporation, precipitation, fluid flux, record |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
THIS RESOURCE IS NO LONGER IN SERVICE. | SciRes_000127 | ftp://ftp.ncdc.noaa.gov/pub/data/paleo/softlib/hibal/hibal.txt | SCR_002461 | Hydrologic Isotopic Balance, HIBAL Hydrologic Isotopic Balance Model for Paleolake Systems | 2026-07-25 12:05:27 | 0 | ||||||
|
University of Arizona; Arizona; USA Resource Report Resource Website 1+ mentions |
University of Arizona; Arizona; USA (RRID:SCR_002459) | UA | university | Public research university in Tucson, Arizona that offers undergraduate and graduate degree programs in psychology, audiology, speech pathology, and medicine. | public research university, arizona |
is related to: University of Arizona CBC Glassblowing Core Facility is parent organization of: Bio Resource for Array Genes Database is parent organization of: Plantagora is parent organization of: Center for Gamma Ray Imaging is parent organization of: TCW is parent organization of: Bird Base is parent organization of: Arizona Cancer Center Tumor Bank is parent organization of: Tree of Life Web Project is parent organization of: HIV and its Coreceptors is parent organization of: Arizona Center for Education and Research on Therapeutics is parent organization of: AGI is parent organization of: GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database is parent organization of: UA Neuroscience GIDP is parent organization of: ChromDB- the chromatin database is parent organization of: Newbler is parent organization of: Arizona Genetics Core is parent organization of: UA Department of Chemistry and Biochemistry Labs and Facilities is parent organization of: University of Arizona Labs and Facilities is parent organization of: UA Infectious Disease Resource Core is parent organization of: University of Arizona Nuclear Magnetic Resonance Core Facility is parent organization of: PhenoGO is parent organization of: FlyBrain is parent organization of: MIRROR: FlyBrain, An Online Atlas and Database of the Drosophila Nervous System is parent organization of: CyVerse is parent organization of: iMicrobe is parent organization of: Arizona University Genetics Core Facility is parent organization of: University of Arizona Molecular Structures Core Facility is parent organization of: University of Arizona Electron Photoemission Spectroscopy and Imaging Laboratory for Observation at the Nanoscale Core Facility is parent organization of: University of Arizona Xray Diffraction Core Facility is parent organization of: University of Arizona Laboratory for Electron Spectroscopy and Surface Analysis Core Facility is parent organization of: University of Arizona W.M. Keck Center for Nano Scale Imaging Core Facility is parent organization of: University of Arizona Electron Paramagnetic Resonance Core Facility is parent organization of: University of Arizona CBC Electronics Core Facility is parent organization of: University of Arizona CBC Machine Shop Core Facility is parent organization of: University of Arizona Imaging Cores Electron Core Facility is parent organization of: University of Arizona Imaging Cores Optical Core Facility is parent organization of: University of Arizona Analytical and Biological Mass Spectrometry Core Facility is parent organization of: University of Arizona Functional Genomics Core Facility is parent organization of: University of Arizona Flow Cytometry and Human Immune Monitoring Shared Resource Core Facility is parent organization of: University of Arizona Phenotyping Core Facility is parent organization of: Planet Microbe is parent organization of: University of Arizona Molecular Clinical Core Facility |
Free | ISNI:0000 0001 2168 186X, grid.134563.6, nlx_13022, Crossref funder ID:100007899, Wikidata:Q503419 | https://ror.org/03m2x1q45 | SCR_002459 | U of A, University of Arizona, UofA | 2026-07-25 12:05:22 | 2 | ||||||
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RepARK Resource Report Resource Website 1+ mentions |
RepARK (RRID:SCR_002333) | software resource | Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome. | standalone software | is listed by: OMICtools | PMID:24634442 | OMICS_03446 | SCR_002333 | Repetitive motif detection by Assembly of Repetitive K-mers | 2026-07-25 12:05:24 | 7 |
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