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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | web service, data access protocol, software resource, data analysis service, production service resource, service resource, analysis service resource | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NHGRI HG005998; NIGMS P50 GM071508 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-08-05 10:46:53 | 7 | ||||||||
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TissueAtlas Resource Report Resource Website 10+ mentions |
TissueAtlas (RRID:SCR_017352) | data or information resource, data access protocol, software resource, database, atlas, web service | Human miRNA tissue atlas. Database showing distribution of miRNA expression across human tissues. | Human, miRNA, tissue, atlas, data, distribution, expression | has parent organization: Saarland University; Saarbrucken; Germany | Saarland University ; Germany ; Siemens Healthcare ; FP7 project BestAgeing |
PMID:26921406 | Free, Freely available | SCR_017352 | 2026-08-05 10:46:46 | 29 | ||||||||
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clusterExperiment Resource Report Resource Website |
clusterExperiment (RRID:SCR_017439) | data processing software, software application, data visualization software, data analysis software, software resource | Software open source R package for executing, evaluating and visualizing different clusterings of experimental data, including data from single cell RNA-Seq studies. Software for running and comparing different clusterings of single cell sequencing data. | Executing, evaluating, visualizing, clustering, experimental, data, single, cell, RNAseq, sequencing, gene, expression, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH U19 MH114830; NIMH U01 MH105979; Chan Zuckerberg Initiative ; ENS-CFM Data Science Chair |
PMID:30180157 | Free, Available for download, Freely available | SCR_017439 | 2026-08-05 10:46:51 | 0 | ||||||||
|
HmtPhenome Resource Report Resource Website |
HmtPhenome (RRID:SCR_017289) | data or information resource, data processing software, software application, data visualization software, network graph visualization software, database, software resource, service resource | Collection of data about variants, genes, phenotypes and diseases involved in mitochondrial functionality. Users can search for variant position, gene, phenotype or disease and retrieve all related information through integrated network of biological entities. | mitochondria, variant, gene, function, phenotype, data |
uses: Human Phenotype Ontology uses: Ensembl uses: OMIM uses: Orphanet uses: DisGeNET has parent organization: University of Bari; Bari; Italy |
DOI:10.1101/660282 | Free, Freely available | SCR_017289 | 2026-08-05 10:46:49 | 0 | |||||||||
|
Tissue Mapper Resource Report Resource Website 1+ mentions |
Tissue Mapper (RRID:SCR_017321) | data processing software, segmentation software, image analysis software, software application, 3d visualization software, data visualization software, image reconstruction software, software resource | Software for comprehensive annotation and delineation of tissue structures by MBF Bioscience. Creates 3D model from image data and annotates regions of interest from customizable ontology list. Map images acquired with brightfield, confocal, two-photon, widefield fluorescence, or light sheet microscopes. | MBF Bioscience, annotation, delineation, mapping, 3D model, image, data, tissue, structure | is used by: SPARC Portal | Restricted | SCR_017321 | Tissue MapperTM, Tissue Mapper | 2026-08-05 10:46:45 | 4 | |||||||||
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Relacs Resource Report Resource Website 1+ mentions |
Relacs (RRID:SCR_017280) | data processing software, data acquisition software, software application, data analysis software, software resource | Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings. | data, acquisition, analysis, electrophysiology, neuronal, response, control, stimulation | Free, Available for download, Freely available | SCR_017280 | Control, and Stimulation, Relaxed Electrophysiological Data Acquisition | 2026-08-05 10:46:45 | 2 | ||||||||||
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Vesselucida 360 Resource Report Resource Website 1+ mentions |
Vesselucida 360 (RRID:SCR_017320) | VL360 | data processing software, segmentation software, image analysis software, software application, 3d visualization software, data visualization software, data analysis software, software resource | Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience. | MBF Bioscience, vasculature, reconstruction, image, analysis, 3D, vessel, data, automatic, quantify, anastomoses, microvascular |
is used by: SPARC Portal works with: Vesselucida Explorer |
Restrcited | https://learn.mbfbioscience.com/vle.html | SCR_017320 | Vesselucida 360, Vesselucida | 2026-08-05 10:46:50 | 2 | |||||||
|
NOVOPlasty Resource Report Resource Website 100+ mentions |
NOVOPlasty (RRID:SCR_017335) | data processing software, image analysis software, software application, alignment software, software resource | Software package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data. | de novo, assembler, heteroplasmy, variance, caller, short, circular, genome, organelle, whole, data | is listed by: OMICtools | Interuniversity Institute of Bioinformatics in Brussels ; Belgian Kids Fund ; Hôpital Universitaire des Enfants Reine Fabiola |
PMID:28204566 | Free, Available for download, Freely available | SCR_017335 | 2026-08-05 10:46:46 | 161 | ||||||||
|
Silver Lab Microscopy Software Resource Report Resource Website 1+ mentions |
Silver Lab Microscopy Software (RRID:SCR_017456) | data processing software, data acquisition software, software application, data visualization software, software resource | Software for use with compact Acousto-Optic Lens Microscope (AOLM) developed in the Silver Lab at UCL. Written in LabVIEW. Performs multiple imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches and points. It comes with tools for visualising data acquired with system. | Imaging, visualising, electrophysiological, data, acousto, optic, lens, microscope, Silver Lab, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University College London; London; United Kingdom |
NINDS NS099689 | Free, Available for download, Freely available | http://silverlab.org/software-resources/ | SCR_017456 | 2026-08-05 10:46:51 | 2 | ||||||||
|
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 | |||||||||
|
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 | |||||||
|
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 | |||||
|
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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