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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | data processing software, data or information resource, software application, software resource | Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed. | Single, cell, RNA-seq, data, gene, list, build, index, organize |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | https://genat.uk/post/scfind/, http://bioconductor.org/packages/scfind/, https://github.com/hemberg-lab/scfind | SCR_017339 | 2026-08-05 10:46:46 | 1 | |||||||||
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MRspa Resource Report Resource Website 10+ mentions |
MRspa (RRID:SCR_017292) | software resource, data processing software, software application, data analysis software | Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab. | post, process, magnetic, resonance, spectroscopy, data, analysis |
has parent organization: University of Minnesota Twin Cities; Minnesota; USA works with: MATLAB |
Restricted | SCR_017292 | Magnetic Resonance signal processing and analysis | 2026-08-05 10:46:53 | 19 | |||||||||
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FoXS Resource Report Resource Website 10+ mentions |
FoXS (RRID:SCR_017269) | web service, data access protocol, software resource, production service resource, service resource, analysis service resource | Web server for computing theoretical scattering profile of structure and fitting of experimental profile. Computes SAXS profile of given atomistic model and fits it to experimental profile. Used for structural modeling applications with small angle X-ray scattering data. | computing, theoretical, scattering, profile, structure, fitting, small, angle, X ray, data | has parent organization: University of California at San Francisco; California; USA | Weizmann Institute Advancing Women in Science ; NIGMS R01 GM083960; NCRR U54 RR022220; NIGMS R01 GM105404; Rinat (Pfizer) Inc. ; Lawrence Berkeley National Lab IDAT program ; NIGMS P41 GM109824 |
PMID:23972848 PMID:27151198 |
Free, Available for download, Freely available | SCR_017269 | Fast X-Ray Scattering | 2026-08-05 10:46:49 | 20 | |||||||
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Kinetic Models of Biological Systems (KiMoSys) Resource Report Resource Website 1+ mentions |
Kinetic Models of Biological Systems (KiMoSys) (RRID:SCR_017423) | data repository, data access protocol, software resource, storage service resource, service resource, web service | Web application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community. | Quantitative, kinetic, model, biological, system, data, storage, search, exchange, experiment |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
EU ; Portuguese national funding agency for science ; research and technology. |
Restricted | r3d100011562 | https://doi.org/10.17616/R3864V | https://fairsharing.org/FAIRsharing.6erywc | SCR_017423 | , Kinetic Models of Biological Systems (KiMoSys), KInetic MOdels of biological SYStems, KiMoSys | 2026-08-05 10:46:54 | 1 | |||||
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Glimma Resource Report Resource Website 10+ mentions |
Glimma (RRID:SCR_017389) | data processing software, software application, data visualization software, data analysis software, software resource | Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data. | Interactive, graphic, gene, expression, analysis, visualisation, RNAseq, data |
uses: LIMMA uses: edgeR uses: DESeq2 |
NHMRC ; Viertel Fellowship ; Victorian State Government Operational Infrastructure Support and Australian Government |
PMID:28203714 | Free, Available for download, Freely available | SCR_017389 | 2026-08-05 10:46:53 | 23 | ||||||||
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HomoplasyFinder Resource Report Resource Website 1+ mentions |
HomoplasyFinder (RRID:SCR_017300) | data processing software, software application, data analysis software, software toolkit, standalone software, software resource | Software tool to identify and annotate homoplasies on phylogeny and sequence alignment. Used to automatically identify any homoplasies present in simulated and real phylogenetic data. Java application that can be used as standalone tool or within statistical programming environment R. | homoplasy, phylogeny, sequence, alignment, identify, data, annotate | Science Foundation Ireland | PMID:30663960 | Free, Available for download, Freely available | https://github.com/JosephCrispell/homoplasyFinder | SCR_017300 | 2026-08-05 10:46:53 | 4 | ||||||||
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The Decoding Toolbox Resource Report Resource Website 10+ mentions |
The Decoding Toolbox (RRID:SCR_017424) | TDT | software resource, data processing software, software application, data analysis software | Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data. | Multivariate, analysis, structural, MRI, data, functional, imaging, brain | German Ministry of Education and Research ; German Research Foundation |
PMID:25610393 | Free, Available for download, Freely available | SCR_017424 | 2026-08-05 10:46:51 | 13 | ||||||||
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Inorganic Crystal Structure Database (ICSD) Resource Report Resource Website 1+ mentions |
Inorganic Crystal Structure Database (ICSD) (RRID:SCR_017429) | ICSD | data or information resource, data repository, database, storage service resource, service resource | Database for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research. | Inorganic, crystal, structure, data, atomic, coordinate, quality, FIZ Karlsruhe — Leibniz Institute for Information Infrastructure |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Restricted | r3d100010085 | http://www2.fiz-karlsruhe.de/icsd_home.html, https://doi.org/10.17616/R3GW2V | SCR_017429 | Inorganic Crystal Structure Database, Inorganic Crystal Structure Database (ICSD), ICSD | 2026-08-05 10:46:51 | 6 | ||||||
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SequelQC Resource Report Resource Website 1+ mentions |
SequelQC (RRID:SCR_017279) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data. | raw, data, PacBio, Sequel, analysis, sequence, DNA, read, length, plot | NSF Plant Genome Research Program IOS-1744001 | DOI:10.1101/611814 | Free, Freely available, Available for download | SCR_017279 | 2026-08-05 10:46:49 | 2 | |||||||||
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QtiPlot Resource Report Resource Website 10+ mentions |
QtiPlot (RRID:SCR_017311) | software resource, data processing software, software application, data analysis software | Software tool for data analysis and scientific visualization by IONDEV SRL. | data, analysis, visualization, IONDEV SRL | Restricted | SCR_017311 | 2026-08-05 10:46:50 | 28 | |||||||||||
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Human Neocortical Neurosolver Resource Report Resource Website 10+ mentions |
Human Neocortical Neurosolver (RRID:SCR_017437) | HNN | data processing software, software application, simulation software, data analysis software, software resource | Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data. | Neural, modeling, human, imaging, data, EEG, MEG, electrical, neocortical, cell, circuit, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Debian is listed by: bio.tools has parent organization: Brown University; Rhode Island; USA has parent organization: Yale University; Connecticut; USA has parent organization: Massachusetts General Hospital |
NIBIB R01 EB022889; NIDCD R01 DC012947 |
DOI:10.1101/740597 | Free, Available for download, Freely available | SCR_017678, biotools:HNN | https://github.com/jonescompneurolab/hnn, https://github.com/jonescompneurolab/hnn/tree/0.0.5, https://github.com/jonescompneurolab/hnn/tree/0.1.2, https://zenodo.org/record/2394296#.Xg4rCEdKiM9, https://bio.tools/HNN | SCR_017437 | 2026-08-05 10:46:47 | 13 | |||||
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SCÅTTER Resource Report Resource Website 50+ mentions |
SCÅTTER (RRID:SCR_017271) | web service, data access protocol, software resource, production service resource, service resource, analysis service resource | Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets. | analysis, data, dataset, small, angle, X ray, scattering, SAXS, BIOISIS | Department of Energy Office of Science Integrated Diffraction Analysis Technologies ; National Cancer Institute Structural Cell Biology of DNA Repair Machines ; National Institute of General Medical Sciences project MINOS |
Restricted | https://bl1231.als.lbl.gov/scatter/ | SCR_017271 | 2026-08-05 10:46:53 | 84 | |||||||||
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NIH Figshare Archive Resource Report Resource Website 1+ mentions |
NIH Figshare Archive (RRID:SCR_017580) | NIH Figshare | data or information resource, data repository, database, storage service resource, service resource | Repository to make datasets resulting from NIH funded research more accessible, citable, shareable, and discoverable. Data submitted will be reviewed to ensure there is no personally identifiable information in data and metadata prior to being published and in line with FAIR -Findable, Accessible, Interoperable, and Reusable principles. Data published on Figshare is assigned persistent, citable DOI (Digital Object Identifier) and is discoverable in Google, Google Scholar, Google Dataset Search, and more.Complited on July,2020. Researches can continue to share NIH funded data and other research product on figshare.com. | Respository, data, NIH funded, data set, FAIR |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: FigShare is related to: FigsharePlus |
NIH | Restricted | SCR_017580 | NIH, Figshare, Fig Share, NIH Figshare, NIH Fig share, National Institute of Health | 2026-08-05 10:46:52 | 9 | |||||||
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Mousebytes Resource Report Resource Website 1+ mentions |
Mousebytes (RRID:SCR_017904) | data or information resource, data repository, database, storage service resource, service resource | Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available. | Data, mouse, cognition, imaging, genomics, integration, bio.tools, OpenBehavior |
is listed by: Debian is listed by: bio.tools is listed by: OpenBehavior has parent organization: Western University; Ontario; Canada |
Weston Brain Institute (Canada) ; Canadian Institute of Health Research ; NSERC ; Alzheimer’s Society of Canada ; Canadian First Research Excellence Fund (BrainsCAN) ; Brain Canada |
PMID:31825307 | Free, Freely available | SCR_021549, SCR_021598, r3d100013886, biotools:Mousebytes | https://bio.tools/MouseBytes, https://edspace.american.edu/openbehavior/project/touchscreen-cognition-mousebytes/, https://doi.org/10.17616/R31NJN7I | SCR_017904 | MouseBytes | 2026-08-05 10:46:58 | 4 | |||||
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Clowder Resource Report Resource Website |
Clowder (RRID:SCR_017599) | data repository, data management software, software application, software resource, storage service resource, service resource | Web based data management system that allows users to share, annotate, organize and analyze large collections of datasets. Software tool for creating some metadata about software tools automatically. Open source data management for long tail data. Provides support for extensible metadata annotation and distributed analytics for automatic curation of uploaded data. Open source software that can be customized and deployed on your own cloud. | Share, annotate, organize, analyze, metadata, long, tail, data, management, custom | has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA | Restricted | https://github.com/clowder-framework | SCR_017599 | 2026-08-05 10:46:52 | 0 | |||||||||
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iBright Analysis Software Resource Report Resource Website 10+ mentions |
iBright Analysis Software (RRID:SCR_017632) | data processing software, image analysis software, software application, data analysis software, software resource | Software for organizing and analyzing blot and gel images captured on iBright Imaging Systems. Available as desktop version PC and Mac OS compatible and cloud-based version accessible via web browser through Connect platform. | Invitrogen, image, adjustment, data, analysis, blot, gel, iBright Imaging System | Free, Available for download, Freely available | SCR_017632 | 2026-08-05 10:46:52 | 17 | |||||||||||
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Structure Harvester Resource Report Resource Website 100+ mentions |
Structure Harvester (RRID:SCR_017636) | web service, data access protocol, software resource, production service resource, service resource, analysis service resource | Web based program for collating results generated by program STRUCTURE. Provides assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of number of genetic groups that best fit data. Reformats data for use in downstream programs, such as CLUMPP.It is complement for using software Structure in genetics population. Website and program for visualizing STRUCTURE output and implementing Evanno method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Visualizing, STRUCTURE, Evanno, method, collating, result, detection, genetic, group, fit, data, reformat |
is related to: University of California at Santa Cruz; California; USA is related to: University of California at Irvine; California; USA is related to: University of California at Los Angeles; California; USA works with: STRUCTURE |
NCI U24 CA143858; NCI R21 CA135937 |
DOI:10.1007/s12686-011-9548-7 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017636 | StructureHarvester | 2026-08-05 10:46:49 | 297 | |||||||
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VG Studio MAX Resource Report Resource Website 10+ mentions |
VG Studio MAX (RRID:SCR_017997) | data processing software, software application, data visualization software, data analysis software, software resource | Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data. | Computed tomography, CT, data, analysis, processing, 3D, visualization, CT data | Restricted | SCR_017997 | VGStudio MAX, VG Studio MAX 3.1, VGStudio | 2026-08-05 10:46:59 | 11 | ||||||||||
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AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | data or information resource, database, production service resource, service resource, analysis service resource | Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers. | Genomic, functional, database, Entamoeba, Acanthamoeba, parasite, microarray, expression, data, experimental, isolate, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Eukaryotic Pathogen Database Resources |
NIDA ; Department of Health and Human Services ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb, https://doi.org/10.17616/R3PX9Q | SCR_017592 | 2026-08-05 10:46:52 | 7 | ||||||
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TIGS Resource Report Resource Website 1+ mentions |
TIGS (RRID:SCR_017565) | data or information resource, data repository, training material, narrative resource, storage service resource, service resource, workflow | Repository to share analysis procedure, data and help readers or reviewers to know more detail of this work, reproduce or make use of results they are interested in. | Share, analysis, procedure, data, tumor, immunogenicity | Free, Available for download, Freely available | SCR_017565 | Tumor Immunogenicity Score | 2026-08-05 10:46:52 | 1 |
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