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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MaAsLin2 Resource Report Resource Website 100+ mentions |
MaAsLin2 (RRID:SCR_023241) | software resource, software toolkit | SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. | Microbiome Multivariable Associations with Linear Models, | NHGRI R01HG005220; NIAID U19AI110820; NIDDK R24DK110499; NIDDK U54DK102557; NSF DEB-2028280 |
DOI:10.1371/journal.pcbi.1009442 | Free, Available for download, Freely available | https://huttenhower.sph.harvard.edu/maaslin/ | SCR_023241 | 2026-09-12 01:03:04 | 212 | ||||||||
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AmpliconArchitect Resource Report Resource Website 50+ mentions |
AmpliconArchitect (RRID:SCR_023150) | software resource, software toolkit | 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 | NHGRI HG010149; NIGMS R01GM114362; NSF NSF-DBI-1458557 |
DOI:10.1038/s41467-018-08200-y | SCR_023150 | 2026-09-12 01:03:03 | 53 | ||||||||||
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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 | NIDA DK097771; NIGMS R01GM113952; NSF III1755761 |
PMID:34415323 | Free, Available for download, Freely available | SCR_022976 | Omics Generative Adversarial Network | 2026-09-12 01:03:02 | 1 | ||||||||
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VirusDetect Resource Report Resource Website 10+ mentions |
VirusDetect (RRID:SCR_023669) | software resource, software toolkit | Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs. | Virus discovery, analyze large scale sRNA datasets, virus identification, deep sequencing of small RNAs, sequencing, small RNAs | NSF | PMID:27825033 | Free, Available for download, Freely available | https://github.com/kentnf/VirusDetect | SCR_023669 | 2026-09-12 01:03:05 | 18 | ||||||||
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rockd Resource Report Resource Website |
rockd (RRID:SCR_024431) | data or information resource, database | Map database allows to record your geological observations and uses your location to provide spatially informed suggestions for nearby geologic units, time intervals, and fossils. | Map database, record geological observations, | NSF ; UW Geoscience |
Free, Freely available | SCR_024431 | 2026-09-12 01:03:08 | 0 | ||||||||||
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Lamont-Doherty Core Repository Resource Report Resource Website |
Lamont-Doherty Core Repository (RRID:SCR_002216) | LDEO-DSSR, LDCR | access service resource, core facility, service resource | Core repository and one of the world's most unique and important collections of scientific samples from the deep sea. Sediment cores from every major ocean and sea are archived at the Core Repository. The collection contains approximately 72,000 meters of core composed of 9,700 piston cores; 7,000 trigger weight cores; and 2,000 other cores such as box, kasten, and large diameter gravity cores. They also hold 4,000 dredge and grab samples, including a large collection of manganese nodules, many of which were recovered by submersibles. Over 100,000 residues are stored and are available for sampling where core material is expended. In addition to physical samples, a database of the Lamont core collection has been maintained for nearly 50 years and contains information on the geographic location of each collection site, core length, mineralogy and paleontology, lithology, and structure, and more recently, the full text of megascopic descriptions. Samples from cores and dredges, as well as descriptions of cores and dredges (including digital images and other cruise information), are provided to scientific investigators upon request. Materials for educational purposes and museum displays may also be made available in limited quantities when requests are adequately justified. Various services and data analyses, including core archiving, carbonate analyses, grain size analyses, and RGB line scan imaging, GRAPE, P-wave velocity and magnetic susceptibility runs, can also be provided at cost. The Repository operates a number of labs and instruments dedicated to making fundamental measurements on material entering the repository including several non-destructive methods. Instruments for conducting and/or assisting with analyses of deep-sea sediments include a GeoTek Multi-Sensor Core Logger, a UIC coulometer, a Micromeritics sedigraph, Vane Shear, X-radiograph, Sonic Sifter, freeze dryer, as well as a variety of microscopes, sieves, and sampling tools. They also make these instruments available to the scientific community for conducting analyses of deep-sea sediments. If you are interested in borrowing any field equipment, please contact the Repository Curator. | deep sea, sediment, ocean, sea, geoscience, metadata |
is listed by: CINERGI is listed by: DataCite is listed by: re3data.org has parent organization: Columbia University; New York; USA |
NSF ; Lamont -Doherty Earth Observatory |
Free, Freely available | DOI:10.26022, DOI:10.17616/R3PV10, nlx_154738 | https://doi.org/10.17616/R3PV10, https://doi.org/10.17616/r3pv10, https://doi.org/10.26022/, https://dx.doi.org/10.26022/ | SCR_002216 | LDEO-Deep Sea Sample Repository, LDEO Core Repository, Lamont -Doherty Earth Observatory | 2026-09-12 01:03:12 | 0 | |||||
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National Lacustrine Core Facility Resource Report Resource Website |
National Lacustrine Core Facility (RRID:SCR_002215) | LacCore | access service resource, core facility, service resource | Archive of almost 20,000 meters of high quality sediment cores from large and small expeditions to lakes all around the world. LacCore advocates for, coordinates, and facilitates core-based research on Earth's continents through collaborative support for logistics, field and laboratory, and data and sample curation and dissemination. They provide a wide variety of fee-based analytical services, as well as offer training and instrument time to lab visitors. They also develop Standard Operating Procedures (SOPs) for local training and adoption by individuals at other labs. | lacustrine, lake, sediment, climate, environment, biota, microscopic, microscopy, marine, mineral, mineraloid, metadata |
is listed by: CINERGI has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NSF EAR-1226265 | Free, Freely available | nlx_154737 | SCR_002215 | Limnological Research Center LacCore Facility, LRC LacCore Facility | 2026-09-12 01:03:12 | 0 | ||||||
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National High Magnetic Field Laboratory High B/T Core Facility Resource Report Resource Website |
National High Magnetic Field Laboratory High B/T Core Facility (RRID:SCR_017360) | B/T | access service resource, core facility, service resource | Facility to conduct experiments in high magnetic fields up to 15 tesla and at very low temperatures down to 0.4 mK simultaneously. Located at University of Florida in Gainesville, it is operated as part of Physics Department Microkelvin Laboratory. | Magnetic, field, temperature | is related to: University of Florida; Florida; USA | Department of Defense ; Department of Energy ; Florida State ; NIH ; NSF DMR-1644779 |
Restricted | SCR_017360 | NHMF Laboratory High B/T Facility, High B/T (magnetic field / temperature) Facility, High B/T Facility | 2026-09-12 01:03:59 | 0 | |||||||
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National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility Resource Report Resource Website 500+ mentions |
National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility (RRID:SCR_017362) | AMRIS | access service resource, core facility, service resource | National High Magnetic Field Laboratory (MagLab) site. It provides researchers with advanced NMR, MRI, and spectroscopy tools (human/animal imaging) for biomedical studies, specializing in high-field magnetic resonance technology. Hosts spectrometers and scanners, including high-field NMR (up to 1.5 GHz), MR microscopy, and human/animal MRI systems (e.g., 3T and 900 MHz). Offers expertise in high-resolution solution NMR, solid-state NMR, and specialized imaging for in vivo animal models and humans.Features an RF coil lab that designs, builds, and tests custom MRI/NMR coils to optimize data collection. Supports research into Alzheimer's, cancer, metabolism, and brain development. | Nuclear Magnetic Resonance, Magnetic Resonance Imaging, spectroscopy, magnetic resonans, scanner, magnet |
has parent organization: National High Magnetic Field Laboratory has parent organization: University of Florida; Florida; USA |
Department of Defense ; Department of Energy ; NSF DMR-1157490; NSF DMR-1644779; NSF DMR-2128556; State of Florida |
Restricted | SCR_017363 | https://nationalmaglab.org/user-facilities/nmr-mri, https://nationalmaglab.org | SCR_017362 | , Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Facility | 2026-09-12 01:03:59 | 859 | |||||
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University of Delaware BioImaging Center Core Facility Resource Report Resource Website 1+ mentions |
University of Delaware BioImaging Center Core Facility (RRID:SCR_017814) | access service resource, core facility, service resource | Microscopy facility that houses equipment including confocal microscopes: LSM780 confocal microscope (Located at CBBI),LSM880 confocal microscope (Located at DBI 117),electron microscopes and their accessory instrumentation:Thermo Scientific Apreo VS SEM microscope,Hitachi S-4700, Leica EM ACE600 and Tousimis Autosamdri-815B,CX7 high content analysis system. Our staff has technical expertise across different microscopy platforms and methodologies. | Microscopy, bioimaging, confocal, electron, microscope, analysis, service, core |
is listed by: ABRF CoreMarketplace has parent organization: University of Delaware; Delaware; USA |
NCRR S10 RR027273; NIGMS P20 GM103446; NIGMS P20 GM113125; NIH Office of the Director S10 OD016361; NIH Office of the Director S10 OD025165; NSF IIA 1301765; State of Delaware |
Open | ABRF_537 | https://coremarketplace.org/?FacilityID=537&citation=1 | SCR_017814 | Delaware University BioImaging Center Core Facility, University of Delaware Bio-Imaging Center | 2026-09-12 01:04:02 | 1 | ||||||
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Delaware University Surface Analysis Core Facility Resource Report Resource Website |
Delaware University Surface Analysis Core Facility (RRID:SCR_017796) | access service resource, core facility, service resource | Core provides consulting and services in X-ray Photoelectron Spectroscopy (XPS or ESCA), Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS), X-ray Photoelectron Imaging, Auger Electron Spectroscopy (AES), Scanning Auger Microscopy or Imaging (SAM), Secondary-Electron Microscopy (SEM), Ion-Scattering Spectroscopy (ISS or LEIS), Scanning Probe Microscopy (STM and AFM). | Surface, analysis, X-ray, photoelectron, spectroscopy, ion, mass, spectrometry, imaging, Auger, microscopy, scattering, scanning, probe, service, core | NSF | Open | ABRF_439 | SCR_017796 | Surface Analysis Facility | 2026-09-12 01:04:02 | 0 | ||||||||
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Northwestern University Central Laboratory for Materials Mechanical Properties Core Facility Resource Report Resource Website 1+ mentions |
Northwestern University Central Laboratory for Materials Mechanical Properties Core Facility (RRID:SCR_017877) | CLaMMP | access service resource, core facility, service resource | Core provides mechanical testing machines and accessories for conducting educational, research, and outreach experiments on most solid materials. | Material, mechanical, property, testing, solid, service, core, ABRF | is listed by: ABRF CoreMarketplace | NSF DMR 1720139 | Open | ABRF_727 | SCR_017877 | Central Laboratory for Materials Mechanical Properties | 2026-09-12 01:04:04 | 3 | ||||||
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University of California at Berkeley Cancer Research Laboratory Molecular Imaging Center Core Facility Resource Report Resource Website 50+ mentions |
University of California at Berkeley Cancer Research Laboratory Molecular Imaging Center Core Facility (RRID:SCR_017852) | MIC | access service resource, core facility, service resource | Microscopy core specializing in laser based fluorescence techniques. Offers training and expertise in 20 different microscope systems, including live cell and in vivo imaging, laser scanning (LSM) and spinning disk (SDC) confocal, multi-photon (2p), fluorescent lifetime imaging (FLIM), light-sheet microscopy (SPIM), super resolution (Airyscan), slide scanning and patterned illumination for optogenetic manipulation and readout. Provides offline computer analysis workstations for image processing, visualization and analysis, including GPU workstations. MIC operates in 3 different buildings on campus, with primary locations in Life Sciences Addition (LSA), North-side core in Barker Hall, and small outpost in Li Ka Shing Center for Biomedical and Health Sciences (LKS).Provides equipment in categories:Confocal and multi photon laser scanning microscopes,Spinning disk confocal microscopes,Lightsheet (SPIM) microscopes,Epifluorescence/widefield scopes and Computer workstations. | Molecular, imaging, microscopy, system, laser, based, fluorescent, technique, live, cell, in vivo, slide, scanning, image, processing, visualization, analysis, service, core | Biological Faculty Research Fund ; Fidelity Foundation Award ; Gordon and Betty Moore Foundation ; Helen Wills Neuroscience Institute ; NCRR S10 RR027696; NCRR S10 RR028971; NEI R01 EY015514; NSF DBI 0116016; NSF DBI1041078 |
Open | ABRF_659 | SCR_017852 | CRL Molecular Imaging Center | 2026-09-12 01:04:03 | 70 | |||||||
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PyNWB Resource Report Resource Website 1+ mentions |
PyNWB (RRID:SCR_017452) | software application, software resource | Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information. | Neurodata, stored, NWB, file, share, standardized, data, format, neurophysiology, BRAIN Initiative |
uses: Hierarchical Data Modeling Framework is used by: NWB Explorer is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Common Schema is related to: NWB Inspector |
Allen Institute for Brain Science ; General Electric ; Howard Hughes Medical Institute ; International Neuroinformatics Coordinating Facility ; Kavli Foundation ; NIH BRAIN Initiative R24 MH116922; NSF 0855272 |
PMID:26590340 | Free, Available for downloading, Freely available | https://github.com/NeurodataWithoutBorders/pynwb | https://github.com/AllenInstitute/nwb-api | SCR_017452 | 2026-09-12 01:02:55 | 4 | ||||||
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CellChat Resource Report Resource Website 500+ mentions |
CellChat (RRID:SCR_021946) | software resource, software toolkit | Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets. | inference, visualization, analysis, cell-cell communication, single cell data, intercellular communication networks, single-cell RNA-sequencing data | Howard Hughes Medical Institute ; LEO Foundation ; NIGMS R01 GM123731; NIH P30 AR07504; NIH U01 AR073159; NSF DMS1763272; Pew Charitable Trust ; Simons Foundation ; UC Irvine |
PMID:33597522 | Free, Available for download, Freely available | http://www.cellchat.org/ | SCR_021946 | 2026-09-12 01:02:59 | 753 | ||||||||
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scrible Resource Report Resource Website |
scrible (RRID:SCR_008882) | scrible | software application, software resource | We''re bringing Web-based research into the Internet Era by empowering people to mark up web pages in the browser and manage and collaborate on them online. And that''s just the start... We''ve got much more planned in a variety of areas to help people manage the mounds of info they''re pulling off the Web everyday. Simply drag the scrible bookmarklet to your browser''s Bookmarks toolbar. Click it later to mark up, save or share web pages. Even though the world uses the Internet to research nearly everything for work, school and home (job postings, press releases, Wikipedia articles, medical info, etc.), most folks still use old-school ways of annotating, organizing and sharing online info (printing to mark by hand, copying/pasting into Word, etc.). It''s archaic, laborious and a waste of time. We''re changing that. A bookmarklet is a bookmarked link that, when clicked, adds functionality to your browser. When the scrible Bookmarklet is clicked, it loads the scrible Toolbar atop the current webpage you''re viewing. Adding the scrible Bookmarklet to your browser is a breeze. Simply drag it to your browser''s Bookmarks Toolbar. | annotate, annotation, bookmarklet | NSF | Free | nlx_149634 | SCR_008882 | 2026-09-12 01:02:38 | 0 | ||||||||
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Biological Information Browsing Environment Resource Report Resource Website |
Biological Information Browsing Environment (RRID:SCR_008170) | BIBE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A facility to help novices and experts find information about plants and animals in digital collections. The objectives of the Project are to facilitate access to online flora and fauna by both novices and experts through enhanced indexing, searching, and visualization techniques. Specific search facility and content will be added to help users with different levels of domain knowledge identify species based on the augmentation of professionally developed taxonomic treatments or species descriptions. This is a novel use of taxonomic descriptions. | fauna, flora, animal, biological, description, identification, plant, specie, taxonomic, taxonomy, treatment | has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA | Division of Biological Infrastructure ; Biological Databases and Informatics Program ; Program Director Sylvia Spengler Project ID:DBI-9982849 ; University of Illinois ; Campus Research Board ; NSF |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21046 | SCR_008170 | Biological Information Browsing Environment | 2026-09-12 01:01:58 | 0 | ||||||
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T-REX Resource Report Resource Website 100+ mentions |
T-REX (RRID:SCR_010715) | T-REX | analysis service resource, data analysis service, production service resource, service resource | T-REX is a free, platform-independent online tool that allows for an integrated, rapid, and more robust analysis of T-RFLP data. Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data. Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model. | has parent organization: Cornell University; New York; USA | Microsoft Corporation ; NSF DGE 0221658 |
PMID:19500385 | nlx_89468 | SCR_010715 | T-REX (T-RFLP analysis EXpedited), T-REX: Software for the processing and analysis of T-RFLP data, T-RFLP analysis EXpedited | 2026-09-12 01:02:05 | 122 | |||||||
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CRAVAT Resource Report Resource Website 10+ mentions |
CRAVAT (RRID:SCR_012776) | CRAVAT | analysis service resource, data analysis service, production service resource, service resource | A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis. |
is listed by: OMICtools has parent organization: Johns Hopkins University; Maryland; USA |
Cancer | NCI CA 152432; NSF DBI 0845275; NCI 1U01CA180956-01 |
OMICS_00147 | SCR_012776 | cancer-related analysis of variants toolkit | 2026-09-12 01:02:08 | 30 | |||||||
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Lightning Pose Resource Report Resource Website |
Lightning Pose (RRID:SCR_024480) | software resource, software toolkit | Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools. | OpenBehavior, animal pose estimation algorithm, Bayesian post processing approach, direct video manipulation, | is listed by: OpenBehavior | Gatsby Charitable Foundation ; Irma T Hirschl Trust ; NINDS K99NS128075; NINDS NS075023; NINDS U19NS123716; NSF ; Simons Foundation |
PMID:37162966 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/lightningpose/ | SCR_024480 | 2026-09-12 01:01:18 | 0 |
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