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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PHATE Resource Report Resource Website 1+ mentions |
PHATE (RRID:SCR_027119) | 3d visualization software, data processing software, data visualization software, software application, software resource, source code | Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances. | visualizing high dimensional data, high dimensional data, | NHGRI 1R01HG008383; NICHD F31HD097958; NIGMS R01GM107092; NIGMS R01GM130847; NSF |
PMID:31796933 | Free, Available for download, Freely available, | SCR_027119 | Potential of Heat-diffusion for Affinity-based Transition Embedding | 2026-09-05 06:35:39 | 5 | ||||||||
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MatrixEQTL Resource Report Resource Website 50+ mentions |
MatrixEQTL (RRID:SCR_025513) | data analysis software, data processing software, software application, software resource | Software tool for ultra fast eQTL analysis via large matrix operations. | expression Quantitative Trait Loci, fast eQTL analysis, large matrix operations, | Gillings Innovation Laboratory in Statistical Genomics ; NCI R01 CA138255; NIEHS R01 ES015241; NIMH R01 MH090936; NSF ; US Environmental Protection Agency |
PMID:22492648 | Free, Freely available, | SCR_025513 | Matrix Expression Quantitative Trait Loci | 2026-09-05 06:35:00 | 75 | ||||||||
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ColabFold Resource Report Resource Website 100+ mentions |
ColabFold (RRID:SCR_025453) | software resource, source code | Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding. | prediction of protein structures and complexes, protein folding, protein structure prediction, | Max Planck Society ; National Research Foundation of Korea ; NIAID R21AI156595; NIH Office of the Director DP5OD026389; NSF ; Seoul National University ; University of Göttingen |
PMID:35637307 | Free, Available for download, Freely available | https://github.com/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb | SCR_025453 | 2026-09-05 06:34:59 | 493 | ||||||||
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MorphoSource Resource Report Resource Website 100+ mentions |
MorphoSource (RRID:SCR_025654) | data or information resource, database | Publicly accessible 3D data repository where subject experts, educators, and general public can find, view, interact with, and download 3D and 2D media representing physical objects important to the world’s natural history, cultural heritage, and scientific collections. Media data are contributed by a community that includes museums, institutions, researchers, scholars, and other subject experts who use MorphoSource to archive data, share findings, and increase scholarly impact. Contributed media represent both biological objects such as fossils and representatives of living species, as well as artifacts and objects created by humans that are critical to our shared cultural heritage. | 3D media, 2D media, physical objects, natural history, cultural heritage, scientific collections, shared cultural heritage, | Duke University ; NSF |
Free, Freely available, | r3d100012224 | https://github.com/MorphoSource, https://doi.org/10.17616/R35Q0K | SCR_025654 | 2026-09-05 06:35:04 | 104 | ||||||||
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SomaticSignatures Resource Report Resource Website 1+ mentions |
SomaticSignatures (RRID:SCR_025620) | software resource, software toolkit, source code | Software R package for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments. | R, identifying mutational signatures, single nucleotide variants, high-throughput experiments, | NSF | PMID:26163694 | Free, Available for download, Freely available, | https://github.com/juliangehring/SomaticSignatures | SCR_025620 | 2026-09-05 06:35:03 | 7 | ||||||||
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ezBIDS Resource Report Resource Website 1+ mentions |
ezBIDS (RRID:SCR_025563) | software resource, web application | Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms. | Guided standardization, neuroimaging data, Brain Imaging Data Structure, BIDS conversion tool, convert neuroimaging data, associated metadata, interoperable, BIDS standard, | BRAIN CONNECTS ; Kavli Foundation ; NIBIB R01EB029272; NIBIB R01EB030896; NIMH R01MH133701; NINDS UM1NS132207; NSF ; Spanish Government ; Wellcome Trust |
PMID:38332144 | Free, Freely available | https://brainlife.io/ezbids/, | SCR_025563 | ez Brain Imaging Data Structure | 2026-09-05 06:35:01 | 1 | |||||||
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LinDA Resource Report Resource Website 1+ mentions |
LinDA (RRID:SCR_025966) | data analysis software, data processing software, software application, software resource, source code | Software linear models for differential abundance analysis of microbiome compositional data. Used to tackle compositional effects in differential abundance analysis. It fits linear regression models on centered log2-ratio transformed data, identifies bias term due to transformation and compositional effect, and corrects bias using mode of regression coefficients. It could fit mixed-effect models. | differential abundance analysis, microbiome compositional data, differential abundance analysis, | Mayo Clinic Center for Individualized Medicine ; NIGMS R01GM144351; NSF |
PMID:35421994 | SCR_025966 | Linear models for differential abundance analysis of microbiome compositional data (LinDA), Linear models for differential abundance analysis of microbiome compositional data | 2026-09-05 06:35:10 | 4 | |||||||||
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iDEP: Integrated Differential Expression and Pathway analysis Resource Report Resource Website 10+ mentions |
iDEP: Integrated Differential Expression and Pathway analysis (RRID:SCR_027373) | iDEP | software resource, web application | Integrated web application for differential expression and pathway analysis of RNA-Seq data. | differential expression, pathway analysis, RNA-Seq data, | NIGMS GM083226; NSF ; State of South Dakota |
PMID:30567491 | Free, Freely available | SCR_027373 | 2026-09-05 06:35:46 | 19 | ||||||||
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VenomView Resource Report Resource Website |
VenomView (RRID:SCR_027588) | software application, software resource, standalone software, web application | Open-access, browser-based visualization and summary tool for venom transcriptomic and proteomic data. R Shiny–based interactive application designed as visualization and reporting interface for venom transcriptomic and proteomic data. It enables users to explore annotation metrics, toxin gene families, and quality-control summaries generated by analysis pipelines. While it will eventually serve as part of the VenomsBase front end, VenomView currently operates as standalone prototype. Provides interactive dashboards showing assembly quality, annotation scores, toxin gene families, and functional domains generated by the VenomFlow analysis pipeline. Connected to VenomLanding, VenomView currently features Doryteuthis pealeii (Squid), linking metadata with detailed annotation summaries. The expanded version will include Sepia bandensis (Cuttlefish), Octopus bimaculoides, and arachnid species. | R Shiny–based interactive application, visualization and reporting interface, venom transcriptomic and proteomic data, |
uses: Shiny has parent organization: Harvard University; Cambridge; United States |
NSF | SCR_027588 | 2026-09-05 06:35:52 | 0 | ||||||||||
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T Cell ExTRECT Resource Report Resource Website 1+ mentions |
T Cell ExTRECT (RRID:SCR_027742) | software resource, software toolkit, source code | Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes. | T-cell, T cell receptor excision circle, WES data, hg19 or hg38 aligned genomes, | NCATS UL1TR000100; NCI P30CA023100; NCI R21CA177519; NCI U01CA196406; NHLBI U54HL108460; NIH Office of the Director DP5OD017937; NLM T15LM011271; NSF |
PMID:34497419 | Free, Available for download, Freely available | SCR_027742 | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-09-05 06:35:57 | 1 | ||||||||
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CoMUT Resource Report Resource Website 1+ mentions |
CoMUT (RRID:SCR_027745) | software library, software resource, software toolkit, source code | Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots. | genomic DNA, phenotype, visualizing genomic and phenotypic information, comutation plots, | NCI R01 CA227388; NCI R37 CA222574; NCI U01 CA233100; NIGMS T32 GM008313; NSF |
PMID:32502231 | Free, Available for download, Freely available | SCR_027745 | 2026-09-05 06:35:57 | 4 | |||||||||
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Conos Resource Report Resource Website 1+ mentions |
Conos (RRID:SCR_026381) | software resource, software toolkit, source code | Software R package for joint analysis of multiple single-cell RNA-seq datasets. Used to wire together large collections of single-cell RNA-seq datasets, which allows for both identification of recurrent cell clusters and propagation of information between datasets in multi-sample or atlas-scale collections. | joint analysis of multiple single-cell RNA-seq datasets, multiple single-cell RNA-seq datasets, identification of recurrent cell clusters, propagation of information between datasets, multi-sample, atlas-scale collections, | NHLBI R01HL131768; NSF ; Zimin Foundation |
DOI:10.1038/s41592-019-0466-z | Free, Available for download, Freely available | SCR_026381 | 2026-09-05 06:35:20 | 9 | |||||||||
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Marine Geoscience Data System Resource Report Resource Website 10+ mentions |
Marine Geoscience Data System (RRID:SCR_002164) | MGDS | data repository, service resource, storage service resource | Repository providing free access to marine geophysical data (e.g. bathymetry, seismic data, magnetics, gravity, images) and related land-based data from NSF-funded research conducted throughout the global oceans. Data Portals include GeoPRISMS, MARGINS, Ridge 2000, Antarctic and Southern Ocean Data Synthesis, the Global Multi-Resolution Topography Synthesis, and Seismic Reflection Field Data Portal. Primary data types served are multibeam bathymetric data from the ocean floor, seismic reflection data imaging below the seafloor, and multi-disciplinary ship based data from the Southern Ocean. Other holdings include deep-sea photographic transects, and ultra-high resolution bathymetry, temperature probe data, biological species compilations, MAPR and CTD data. Derived data products and sets include microseismicity catalogs, images, visualization scenes, magnetic and gravity compilations, grids of seismic layer thickness, velocity models, GIS project files, and 3D visualizations. Tools to discover, explore, and visualize data are available. They deliver catalogs, maps, and data through standard programmatic interfaces. GeoMapApp, a standalone data visualization and analysis tool, permits dynamic data exploration from a map interface and the capability to generate and download custom grids and maps and other data. Through GeoMapApp, users can access data hosted at the MGDS, at other data repositories, and import their own data sets. Global Multi-Resolution Topography (GMRT) is a continuously-updated compilation of seafloor bathymetry integrated with global land topography. It can be used to create maps and grids and it can be accessed through several standard programmatic interfaces including GeoMapApp and Google Earth. The GMRT compilation can also be explored in 3D using Virtual Ocean. The MGDS MediaBank contains high quality images, illustrations, animations and video clips that are organized into galleries. Media can be sorted by category, and keyword and map-based search options are provided. Each item in the MediaBank is accompanied by metadata that provides access to a cruise catalog and data repository. | observation, solid earth, ocean, earth, polar sciences, marine, geophysical, bathymetry, seismic, magnetics, gravity, image, geology, bathymetric map, topographic map, mid-ocean ridge, submarine topography, continental margin, continental shelf, continental slope, expedition, catalog, web service, dynamic map |
uses: DataCite is listed by: re3data.org is listed by: CINERGI is related to: PetDB is related to: GeoMapApp has parent organization: Integrated Earth Data Applications is parent organization of: Antarctic and Southern Ocean Data Portal is parent organization of: Academic Seismic Portal at LDEO is parent organization of: U.S. Antarctic Program Data Coordination Center |
NSF | Free, Freely available | r3d100010273, nlx_154713, DOI:10.26022/ | https://doi.org/10.26022/, https://dx.doi.org/10.26022/, https://doi.org/10.17616/R38C83 | SCR_002164 | 2026-09-05 06:24:44 | 18 | ||||||
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International Neuroinformatics Coordinating Facility Resource Report Resource Website 50+ mentions |
International Neuroinformatics Coordinating Facility (RRID:SCR_002282) | INCF | nonprofit organization | Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society. | neuroinformatics, neuroscience, neuroimaging, clinical, brain, data, sharing, reuse, global |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Spike Sorting Evaluation Project is related to: Allen Brain Atlas API is related to: SenseLab has parent organization: Karolinska Institute; Stockholm; Sweden has parent organization: Royal Institute of Technology; Stockholm; Sweden is parent organization of: INCF Dataspace is parent organization of: Waxholm Space is parent organization of: MUlti SImulation Coordinator is parent organization of: INCF Software Center is parent organization of: Program on Ontologies of Neural Structures is parent organization of: Common Upper Mammalian Brain Ontology is parent organization of: INCF Training in Neuroinformatics is parent organization of: INCF Funding is parent organization of: INCF Blog is parent organization of: INCForg - YouTube is parent organization of: INCF Swiss Node is parent organization of: INCF Newsroom is parent organization of: INCF Japan Node is parent organization of: Scalable Brain Atlas is parent organization of: INCF Job Board is parent organization of: INCF Neuroimaging Data Sharing is parent organization of: Waxholm Space is parent organization of: NeuroLex is parent organization of: Neuroimaging Data Model is parent organization of: Neuron Registry Curator Interface is parent organization of: INCF-Neurobot |
NSF ; Swedish Foundation for Strategic Research ; Swedish Research Council |
ISNI: 0000 0004 6107 939X, grid.498423.0, nif-0000-00365 | https://ror.org/02y5xjh56 | SCR_002282 | INCF, International Neuroinformatics Coordinating Facility, The International Neuroinformatics Coordinating Facility | 2026-09-05 06:24:46 | 63 | ||||||
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National Snow and Ice Data Center Resource Report Resource Website 50+ mentions |
National Snow and Ice Data Center (RRID:SCR_002220) | NSIDC | data or information resource, data repository, database, image collection, service resource, storage service resource | National data center / repository for snow and ice data including snow, ice, glaciers, frozen ground, and climate interactions that make up Earth's cryosphere. The center manages and distributes scientific data, creates tools for data access, supports data users, performs scientific research, and educates the public about the cryosphere. Users may explore the Earth's frozen places in the collection of photographs and images. Photographs from field research trips, images captured by satellites of the changing cryosphere, and photos and images are available. Data sets are organized into the following groups: sea ice, frozen ground, snow cover, snow hydrology, glaciers and ice sheets, arctic people. | polar, snow, ice, climate, photo, visualization, sea ice, arctic, meteorology, frozen, antarctica, arctic region, sea ice, satellite, ice sheet, global warming, glacier, frozen ground, cryosphere, climatology, arctic people, snow cover, snow hydrology, catalog, data set, interaction, FASEB list |
is listed by: CINERGI is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: University of Colorado Boulder; Colorado; USA is parent organization of: Antarctic Glaciological Data Center is parent organization of: ACADIS Gateway |
NASA ; NSF ; NOAA |
PMID:32116128 | Public, Unless specifically stated that the information has limitations for its use, Acknowledgement requested, Free, Photos come from a variety of sources, And may have different copyright restrictions and credits. | DOI:10.7265, nlx_154742, DOI:10.25504/FAIRsharing.k9vqye, DOI:10.17616/R3HP4V, DOI:10.5067/ | https://doi.org/10.17616/R31NJMJB, https://doi.org/10.17616/r3HP4V, https://doi.org/10.7265/, https://dx.doi.org/10.7265/, https://fairsharing.org/10.25504/FAIRsharing.k9vqye, https://doi.org/10.5067/, https://dx.doi.org/10.5067/ | SCR_002220 | National Snow & Ice Data Center | 2026-09-05 06:24:45 | 53 | ||||
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OpenTopography Resource Report Resource Website 10+ mentions |
OpenTopography (RRID:SCR_002204) | OpenTopo | data or information resource, data repository, service resource, storage service resource | Accepts and provides access to high-resolution (meter to sub-meter scale) Earth science-oriented topography data (e.g. LiDAR) and bathymetric data, and related tools and resources. The OpenTopography Tool Registry provides a community populated clearinghouse of software, utilities, and tools oriented towards high-resolution topography data (e.g. collected with LiDAR technology) handling, processing, and analysis. Tools registered range from source code to full-featured software applications. Contributions to the registry via the Contribute a Tool page are welcome. OpenTopography also hosts a dataset catalog to which users can register datasets hosted elsewhere; these entries are discoverable by users alongside OpenTopography hosted datasets. Lidar point cloud data are available in LAS, LAZ and ASCII formats. Raster datasets and derived products can be downloaded in Arc ASCII, IMG, and GeoTIFF formats. Derived products and visualizations are available in Google Earth KML format. The OpenTopography user community and advisory committee provides feedback to define the scope of collaborations on data hosting and cyberinfrastructure development | topography, topographical surveying, cloud, earth sciences, aerial photography, topographic map, geography, bathymetric map, geological mapping, geographic information system, bathymetry |
is listed by: CINERGI is listed by: re3data.org is listed by: DataCite has parent organization: San Diego Supercomputer Center has parent organization: University of California; California; USA |
NSF 1948857; NSF 1948994; NSF 1948997 |
Free, Available for download, Freely available | nlx_154717, r3d100010655 | https://api.datacite.org/dois?prefix=10.5069, https://doi.org/10.17616/R3J616 | SCR_002204 | , OpenTopography Facility, Open Topography, NSF OpenTopography Facility | 2026-09-05 06:24:45 | 22 | |||||
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BCO-DMO Resource Report Resource Website 10+ mentions |
BCO-DMO (RRID:SCR_002191) | BCO-DMO | data or information resource, data repository, data set, service resource, storage service resource | Accepts and provides access to marine biogeochemical and ecological data sets from NSF-funded research programs. BCO-DMO is also the data repository for the US GLOBEC and JGOFS programs. | marine, biogeochemical, ecological, ocean, oceanographic, biology, polar |
is listed by: CINERGI has parent organization: Woods Hole Oceanographic Institution; Massachusetts; USA |
NSF | The community can contribute to this resource, For use by the academic and scientific community, Acknowledgement required, See terms of use, Non-commercial, Commercial with written permission | nlx_154701 | SCR_002191 | Biological and Chemical Oceanography Data Management Office, Biological & Chemical Oceanography Data Management Office | 2026-09-05 06:24:45 | 29 | ||||||
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National Center for Earth-Surface Dynamics Resource Report Resource Website |
National Center for Earth-Surface Dynamics (RRID:SCR_002195) | NCED | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Field, laboratory, and model data related to earth-surface dynamics created or compiled by NCED-funded scientists. NCED is a Science and Technology Center developed to predict the coupled dynamics and co-evolution of landscapes and their ecosystems in order to transform management and restoration of the Earth-surface environment. | landscape, ecosystem, data set |
is listed by: CINERGI has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NSF | Free, Freely available | r3d100011295, nlx_154715 | https://doi.org/10.17616/R3XW6D | SCR_002195 | NCED Data Repository | 2026-09-05 06:24:45 | 0 | |||||
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Molecular Simulation Trajectories Archive of a Villin Variant Resource Report Resource Website |
Molecular Simulation Trajectories Archive of a Villin Variant (RRID:SCR_002704) | Molecular Simulation Trajectories Archive of a Villin Variant | d spatial image, data or information resource, data set | An archive of hundreds of all-atom, explicit solvent molecular dynamics simulations that were performed on a set of nine unfolded conformations of a variant of the villin headpiece subdomain (HP-35 NleNle). It includes scripts for accessing the archive of villin trajectories as well as a VMD plug-in for viewing the trajectories. In addition, all starting structures used in the trajectories are also provided. The simulations were generated using a distributed computing method utilizing the symmetric multiprocessing paradigm for individual nodes of the Folding_at_home distributed computing network. The villin trajectories in the archive are divided into two projects: PROJ3036 and PROJ3037. PROJ3036 contains trajectories starting from nine non-folded configurations. PROJ3037 contains trajectories starting from the native (folded) state. Runs 0 through 8 (in PROJ3036) correspond to starting configurations 0 through 8 discussed in the paper in J. Mol. Biol. (2007) 374(3):806-816 (see the publications tab for a full reference), whereas RUN9 uses the same starting configuration as RUN8. Each run contains 100 trajectories (named clone 0-99), each with the same starting configuration but different random velocities. Trajectories vary in their length of time and are subdivided into frames, also known as a generation. Each frame contains around 400 configurational snapshots, or timepoints, of the trajectory, with the last configurational snapshot of frame i corresponding to the first configurational snapshot of generation i+1. The goal is to allow researchers to analyze and benefit from the many trajectories produced through the simulations. | dynamic, atom, headpiece, molecular, simulation, solvent, protein folding, villin, molecule, trajectory, simulation, molecular dynamics trajectory |
is listed by: Biositemaps has parent organization: Simtk.org |
Stanford University; California; USA ; Graduate Fellowship ; NIH ; NIGMS R01-GM062868; NSF MCB-0317072 |
PMID:17950314 | Acknowledgement requested, Available in Gromacs and PDB formats. | nif-0000-23331 | SCR_002704 | 2026-09-05 06:24:52 | 0 | ||||||
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Internet Archive Resource Report Resource Website 50+ mentions |
Internet Archive (RRID:SCR_001682) | IA | audio track, data or information resource, narrative resource, organization portal, portal, software resource, video resource | An Internet library offering the general public access to historical collections that exist in digital format including texts, audio, moving images, and software. Additionally it provides archived web pages in their collections, and specialized services for adaptive reading and information access for the blind and other persons with disabilities. Founded in 1996 and located in San Francisco, the Archive has been receiving data donations from Alexa Internet and others. In late 1999, the organization started to grow to include more well-rounded collections. | audio-visual archive, web archive, software documentation |
is listed by: re3data.org is parent organization of: Personal Archiving |
Alexa Internet ; HP Computer ; The Kahle/Austin Foundation ; Prelinger Archives ; Library of Congress ; LizardTech ; Alfred P. Sloan Foundation ; Individual contributors ; NSF |
Free, Available for download, Freely available | nif-0000-10172 | SCR_001682 | The Internet Archive | 2026-09-05 06:24:37 | 97 |
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