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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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metaRNASeq Resource Report Resource Website 10+ mentions |
metaRNASeq (RRID:SCR_002174) | software resource | Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments. | standalone software, unix/linux, mac os x, windows, r |
is listed by: OMICtools is related to: SMAGEXP has parent organization: CRAN |
PMID:24678608 | Free, Available for download, Freely available | OMICS_03527 | SCR_002174 | SciCrunch Registry | metaRNASeq: Meta-analysis of RNA-seq data | 2026-10-31 12:13:02 | 35 | |||||||
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BioAfrica HIV Informatics in Africa Resource Report Resource Website 1+ mentions |
BioAfrica HIV Informatics in Africa (RRID:SCR_002295) | data or information resource, portal, topical portal | The BioAfrica HIV-1 Proteomics Resource is a website that contains detailed information about the HIV-1 proteome and protease cleavage sites, as well as data-mining tools that can be used to manipulate and query protein sequence data, a BLAST tool for initiating structural analyses of HIV-1 proteins, and a proteomics tools directory. HIV Proteomics Resource contains information about each HIV-1 gene product in regard to expression, post-transcriptional / post-translational modifications, localization, functional activities, and potential interactions with viral and host macromolecules. The Proteome section contains extensive data on each of 19 HIV-1 proteins, including their functional properties, a sample analysis of HIV-1HXB2, structural models and links to other online resources. The HIV-1 Protease Cleavage Sites section provides information on the position, subtype variation and genetic evolution of Gag, Gag-Pol and Nef cleavage sites. | expression, functional, gene, aids, cleavage, database, hiv, hiv/aids databases, interaction, localization, model, modification, post-transcriptional, post-translational, protease, protein, proteome, proteomic, publication, research, sequence, software, structural, journal article | has parent organization: University of KwaZulu-Natal; Durban; South Africa | nif-0000-21050 | SCR_002295 | SciCrunch Registry | HIV Informatics in Africa | 2026-10-31 12:13:04 | 5 | |||||||||
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ARK-Genomics: Centre for Functional Genomics Resource Report Resource Website 10+ mentions |
ARK-Genomics: Centre for Functional Genomics (RRID:SCR_002214) | ARK Genomics | access service resource, core facility, data or information resource, database, organization portal, portal, service resource | Portal for studies of genome structure and genetic variation, gene expression and gene function. Provides services including DNA sequencing of model and non-model genomes using both Next Generation and Sanger sequencing , Gene expression analysis using both microarrays and Next Generation Sequencing, High throughput genotyping of SNP and copy number variants, Data collection and analysis supported in-house high performance computing facilities and expertise, Extensive EST clone collections for a number of animal species, all of commercially available microarray tools from Affymetrix, Illumina, Agilent and Nimblegen, Parentage testing using microsatellites and smaller SNP panels. ARK-Genomics has developed network of researchers whom they support through each stage of their genomics research, from grant application, experimental design and technology selection, performing wet laboratory protocols, through to analysis of data often in conjunction with commercial partners. | gene expression, farm, function, gene, genetic, animal, dna, genome, genomic, genotype, knowledge base, model, structure, variation, job, comparative genome hybridization, parentage testing, microsatellite |
is listed by: ScienceExchange is related to: Roslin Institute Labs and Facilities has parent organization: Roslin Institute works with: University of Edinburgh GenePool Next Generation Sequencing and Bioinformatics |
BBSRC | Free, Freely available | nif-0000-20966, SciEx_157 | https://genomics.ed.ac.uk/ | SCR_002214 | SciCrunch Registry | ARK Genomics, Roslin Institute ARK-Genomics | 2026-10-31 12:13:03 | 13 | |||||
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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 | SciCrunch Registry | University College London Medical School, UCL Medical School | 2026-10-31 12:13:03 | 0 | ||||||||
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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 | Wikidata: Q3100800, ISNI: 0000 0004 0641 2997, grid.434728.e, nif-0000-20957 | https://ror.org/028pnqf58 | SCR_002172 | SciCrunch Registry | Genoscope - Centre National de S�quen�age, Genoscope - French National Sequencing Center, French National Sequencing Center, Genoscope - Centre National de Sequencage | 2026-10-31 12:13:02 | 165 | ||||||
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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 | SciCrunch Registry | demi: Differential Expression from Multiple Indicators, Differential Expression from Multiple Indicators | 2026-10-31 12:13:04 | 6 | ||||||
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EarthChem Resource Report Resource Website 10+ mentions |
EarthChem (RRID:SCR_002207) | EarthChem | data or information resource, data repository, database, service resource, storage service resource | Accepts and makes available geochemical, geochronlogical, and petrological data (analytical and synthesis) through this community-driven effort to facilitate the preservation, discovery, access and visualization of data generated. * PetDB holds geochemical data from sub-oceanic igneous and metamorphic rocks generated at mid-ocean ridges including back-arc basins, young seamounts, and old oceanic crust. Data are compiled primarily from the published literature. * SedDB integrates marine and terrestrial sediment geochemical data compiled primarily from the published literature. * Deep Lithosphere Data Set contains geochemical and petrological data from lower crust and upper mantle xenoliths. (more info) * VentDB contains hydrothermal spring geochemistry that hosts and serves the full range of compositional data acquired on seafloor hydrothermal vents from all tectonic settings. * NAVDAT - The Western North American Volcanic and Intrusive Rock Database * Geochron is an application that helps with the onerous task of data management for geochronological and thermochronological studies. * EarthChemPortal is the one-stop-shop for geochemical data that gives users the ability to search federated databases PetDB, NAVDAT, and GEOROC simultaneously, integrated into a common output format. (more info) * The EarthChem Library is a repository for geochemical datasets (analytical data, experimental data, synthesis databases) and other digital resources relevant to the field of geochemistry, contributed by the geochemistry community. * SESAR - System for Earth SAmple Registration | geochemical, geochronological, petrological |
is listed by: CINERGI has parent organization: Columbia University; New York; USA is parent organization of: VentDB is parent organization of: PetDB is parent organization of: SedDB is parent organization of: System for Earth Sample Registration |
NSF | Free, Available for download, Freely available | nlx_154721, r3d100011538 | https://doi.org/10.17616/R3V644 | SCR_002207 | SciCrunch Registry | IEDA: EarthChem | 2026-10-31 12:13:03 | 30 | |||||
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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 | SciCrunch Registry | flowCore: Basic structures for flow cytometry data | 2026-10-31 12:13:03 | 376 | |||||||
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MetPetDB Resource Report Resource Website 1+ mentions |
MetPetDB (RRID:SCR_002208) | MetPetDB | data or information resource, data repository, database, service resource, storage service resource | Database / data repository for metamorphic petrology that is being designed and built by a global community of metamorphic petrologists in collaboration with computer scientists at Rensselaer Polytechnic Institute as part of the National Cyberinfrastructure Initiative. | metamorphic, petrology, geology, geochemistry |
is listed by: CINERGI has parent organization: Rensselaer Polytechnic Institute; New York; USA |
NSF EAR 0949318 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154722, r3d100012514 | SCR_002208 | SciCrunch Registry | 2026-10-31 12:13:03 | 1 | |||||||
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Human Brain Project EU Resource Report Resource Website 50+ mentions |
Human Brain Project EU (RRID:SCR_002241) | HBP EU, HBP, European HBP, | data or information resource, funding resource, organization portal, portal | Global, collaborative effort for neuroscience, medicine and computing to understand brain, its diseases and its computational capabilities. Goal is to obtain access to research, data sources, platforms and infrastructures offered by other organisations, and enabling organizations outside HBP to use HBP platforms to pursue their own research. Coordinating these activities is the responsibility of the European Research Programme. | brain, ethics, neuroscience, medicine, computing, treatment, brain disease, neuroinformatics, software development, computational modeling, software, connectomics |
is related to: BigBrain is related to: Julich-Brain Cytoarchitectonic Atlas is parent organization of: subcellular application is parent organization of: Subcellular App |
Restricted | nlx_155553 | SCR_002241 | SciCrunch Registry | European Human Brain Project | 2026-10-31 12:13:03 | 69 | |||||||
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edX Resource Report Resource Website 10+ mentions |
edX (RRID:SCR_002240) | edX | online course, training resource | Massive, open, online courses (MOOCs) and interactive online classes in subjects including law, history, science, engineering, business, social sciences, computer science, public health, and artificial intelligence (AI). This non-profit was created by founding partners Harvard and MIT bringing the best of higher education to students around the world. Online courses are designed to be interesting, fun and rigorous. They are the best online courses, from the best professors and the best schools, spanning dozens of subjects. Some edX courses now offer ID verified Certificates of Achievement. A new way to demonstrate your achievement and showcase your knowledge. | education |
has parent organization: Harvard University; Cambridge; United States has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Free, Freely available | nlx_155551 | SCR_002240 | SciCrunch Registry | 2026-10-31 12:13:03 | 22 | ||||||||
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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 | SciCrunch Registry | Compilable Imaging Graphics and Analytical Language | 2026-10-31 12:13:03 | 6 | |||||
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CUAHSI Hydrologic Information System Resource Report Resource Website |
CUAHSI Hydrologic Information System (RRID:SCR_002197) | CUAHSI-HIS, CUAHSI HIS | data access protocol, data analysis software, data or information resource, data processing software, data repository, database, service resource, software application, software resource, storage service resource, web service | An internet-based system for sharing hydrologic data. It is comprised of databases and servers, connected through web services, to client applications, allowing for the publication, discovery and access of data. | hydrologic data, data sharing, water | is listed by: CINERGI | Free, Freely available | r3d100010082, nlx_154706 | http://his.cuahsi.org/ | SCR_002197 | SciCrunch Registry | Consortium of Universities for the Advancement of Hydrologic Science Hydrologic Information System | 2026-10-31 12:13:02 | 0 | ||||||
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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 | SciCrunch Registry | NYU CBI NIfTI Matlab tool | 2026-10-31 12:13:03 | 1 | |||||||
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Community Surface Dynamics Modeling System Resource Report Resource Website |
Community Surface Dynamics Modeling System (RRID:SCR_002196) | CSDMS | computational hosting, data or information resource, data repository, data set, service resource, software resource, storage service resource | Model repository and data related to earth-surface dynamics modeling. The CSDMS Modeling Tool (CMT) allows you to run and couple CSDMS model components on the CSDMS supercomputer in a user-friendly software environment. Components in the CMT are based on models, originally submitted to the CSDMS model repository, and now adapted to communicate with other models. The CMT tool is the environment in which you can link these components together to run new simulations. The CMT software runs on your own computer; but it communicates with the CSDMS HPCC, to perform the simulations. Thus, the CMT also offers you a relatively easy way of using the CSDMS supercomputer for model experiments. CSDMS deals with the Earth's surface - the ever-changing, dynamic interface between lithosphere, hydrosphere, cryosphere, and atmosphere. They are a diverse community of experts promoting the modeling of earth surface processes by developing, supporting, and disseminating integrated software modules that predict the movement of fluids, and the flux (production, erosion, transport, and deposition) of sediment and solutes in landscapes and their sedimentary basins. CSDMS: * Produces protocols for community-generated, continuously evolving, open software * Distributes software tools and models * Provides cyber-infrastructure to promote the quantitative modeling of earth surface processes * Addresses the challenging problems of surface-dynamic systems: self-organization, localization, thresholds, strong linkages, scale invariance, and interwoven biology & geochemistry * Enables the rapid development and application of linked dynamic models tailored to specific landscape basin evolution (LBE) problems at specific temporal and spatial scales * Partners with related computational and scientific programs to eliminate duplication of effort and to provide an intellectually stimulating environment * Supports a strong linkage between what is predicted by CSDMS codes and what is observed, both in nature and in physical experiments * Supports the imperatives in Earth Science research | model, earth, surface, surface dynamics |
is listed by: CINERGI has parent organization: University of Colorado Boulder; Colorado; USA |
NSF | PMID:17406970 | Free, Freely available | r3d100012544, nlx_154705 | https://doi.org/10.17616/R3051W | SCR_002196 | SciCrunch Registry | 2026-10-31 12:13:02 | 0 | |||||
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Neotoma Paleoecology Database Resource Report Resource Website 10+ mentions |
Neotoma Paleoecology Database (RRID:SCR_002190) | Neotoma | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Paleoecology database for plio-pleistocene to holocene fossil data with a centralized structure for interdisciplinary, multiproxy analyses and common tool development; discipline-specific data can also be easily accessed. Data currently include North American Pollen (NAPD) and fossil mammals (FAUNMAP). Other proxies (plant macrofossils, beetles, ostracodes, diatoms, etc.) and geographic areas (Europe, Latin America, etc.) will be added in the near future. Data are derived from sites from the last 5 million years. | data sharing, paleoecology, plio-pleistocene, holocene, fossil |
is listed by: CINERGI has parent organization: Pennsylvania State University |
NSF | Free, Available for download, Freely available | nlx_154700, r3d100011761 | SCR_002190 | SciCrunch Registry | NeotomaDB, Neotoma DB | 2026-10-31 12:13:02 | 38 | ||||||
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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 | SciCrunch Registry | 4D Atlas Construction Toolbox, 4D Atlas Construction | 2026-10-31 12:13:03 | 3 | |||||
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Gene Bridges Resource Report Resource Website 1+ mentions |
Gene Bridges (RRID:SCR_000483) | Gene Bridges | commercial organization | A biotech company that commercializes its patented Red/ET recombination worldwide as licenses and supplies several products for the pharmaceutical and biotech industry as well as academia. It operates from the Technologie Park in Heidelberg and provides customized in-house DNA modification of any kind. Recombineering with Red/ET allows cloning, subcloning and modification of DNA at any chosen position. It permits precise engineering of DNA molecules of any size, including very large ones such as BACs or the E.coli chromosome. | recombineering, red/et recombination, license, dna modification, dna, recombination kit | is related to: AgedBrainSYSBIO | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158134 | SCR_000483 | SciCrunch Registry | Gene Bridges - The Recombineering Company, Gene Bridges GmbH | 2026-10-31 12:12:39 | 3 | |||||||
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miRprimer Resource Report Resource Website 1+ mentions |
miRprimer (RRID:SCR_000480) | miRprimer | software resource | Software tool for automatic design of primers for PCR amplification of microRNAs using the method miR-specific RT-qPCR (Balcells, I., Cirera, S., and Busk, P.K. (2011). Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 11, 70). | ruby, primer, microrna, rt-qpcr, ms windows, pcr amplification |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24472427 | Free, Available for download, Freely available | OMICS_02311 | SCR_000480 | SciCrunch Registry | miRprimer - Automatic design of primers for miR-specific RT-qPCR | 2026-10-31 12:12:39 | 3 | ||||||
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BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | data analysis software, data processing software, data visualization software, software application, software resource | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | SciCrunch Registry | BAIT - Software to help analyse Strand-Seq data | 2026-10-31 12:12:39 | 1 |
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