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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SynapseLocator Resource Report Resource Website 1+ mentions |
SynapseLocator (RRID:SCR_017263) | image processing software, software resource, software application, data processing software | Software tool that combines steps of image processing, non rigid image registration, and spot localisation. Performs registration of 3D imaging data and localization of spots, active synapses in light microscopy images, in semi automatic mode with graphical user interface. | image, processing, registration, spot, localisation, 3D, data, active, synapses, microscopy |
is related to: MATLAB is related to: Fiji |
DOI:https://doi.org/10.1101/538041 | Free, Available for download, Freely available | SCR_017263 | 2026-02-10 09:57:28 | 1 | |||||||||
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Data Information System - DAISY Resource Report Resource Website 1+ mentions |
Data Information System - DAISY (RRID:SCR_017472) | DAISY | web application, software resource | Open source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement. | Map, data, flow, GDPR | Free, Available for download, Freely available | https://github.com/elixir-luxembourg/daisy | SCR_017472 | DAta Information SYstem | 2026-02-10 09:57:30 | 2 | ||||||||
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Fcirc Resource Report Resource Website 1+ mentions |
Fcirc (RRID:SCR_018090) | Fcirc | workflow software, software resource, software application, data processing software | Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs. | Fusion gene, linear and circular RNA, fusion exploration, RNAseq data, linear transcript, circRNA, gene, data, pipeline, bio.tools |
uses: HISAT2 uses: SAMTOOLS is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31771469 ; National Natural Science Foundation of China 31571363 ; National Natural Science Foundation of China 81573023 ; National Key Research and Development Program 2017YFC0908500 |
Free, Available for download, Freely available | biotools:Fcirc | https://bio.tools/Fcirc | SCR_018090 | Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs | 2026-02-10 09:57:42 | 2 | |||||
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Adobe Photoshop Lightroom Resource Report Resource Website 1+ mentions |
Adobe Photoshop Lightroom (RRID:SCR_018012) | image processing software, software resource, software application, data processing software | Camera raw data processing software. Cloud-based service to edit, organize, store, and share photos across any device. | Data, processing, editing, organizing, storing, sharing, photograph, image | is related to: Adobe Photoshop | Restricted | SCR_018012 | 2026-02-10 09:57:42 | 3 | ||||||||||
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SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | web application, software resource | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31701415; National Key Research and Development Program of China 2018YFD0100803; National Key Research and Development Program of China 2016YFD0100801 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/ https://bio.tools/SnpHub |
SCR_018177 | 2026-02-10 09:57:38 | 1 | |||||||
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ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | data visualization software, software resource, software application, data processing software | Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses. | Phylogenetic tree visualization, phylogenetic tree annotation, data, bio.tools |
is listed by: CRAN is listed by: Bioconductor is listed by: Debian is listed by: bio.tools |
Seed Funding Programme for Basic Research | DOI:10.1111/2041-210X.12628 | Free, Available for download, Freely available | biotools:ggtree | https://bio.tools/ggtree | SCR_018560 | 2026-02-10 09:57:44 | 53 | ||||||
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BRAIN Initiative Resource Report Resource Website 10+ mentions |
BRAIN Initiative (RRID:SCR_006770) | NIH BRAIN Initiative | organization portal, portal, data or information resource | Project aimed at revolutionizing understanding of human brain, to show how individual cells and complex neural circuits interact, enable rapid progress in development of new technologies and data analysis tools to treat and prevent brain disorders. BRAIN Initiative encourages collaborations between neurobiologists and scientists from disciplines such as statistics, physics, mathematics, engineering, and computer and information sciences. Institutes and centers contributing to NIH BRAIN Initiative support those research efforts. | brain, connectomics, disorder, cell, neural, circuit, neurotechnology, data, repository, analysis |
uses: Single Cell Portal recommends: Human Neocortical Neurosolver recommends: Brain Gene Expression Analysis toolbox recommends: clusterExperiment recommends: BioWheel recommends: iELVis recommends: Mediation Analysis of Causality under Confounding recommends: MCell recommends: microMS recommends: MIIVsem recommends: MountainSort recommends: Myriads recommends: nelpy recommends: NetPyNE recommends: Neural Ideal recommends: NEURON recommends: Neuron Tools recommends: Neuroscience Gateway recommends: NUTMEG recommends: PetaVision recommends: PyNWB recommends: pyRayleighCuda recommends: ScanImage recommends: Scope recommends: Seizure-Waves recommends: Silver Lab Microscopy Software recommends: StimVision recommends: TReNA recommends: ALICE recommends: BioImage Suite recommends: EyeWire recommends: GIMME recommends: GMA recommends: Homer2 recommends: Brain Image Library recommends: Data Archive BRAIN Initiative recommends: OpenNeuro recommends: Brain Observatory Storage Service and Database (BossDB) recommends: 1000 Functional Connectomes Project recommends: FastProject recommends: Autopatcher recommends: cytoNet recommends: DiffuserCam recommends: gene Expression Analysis Resource recommends: NeMOarchive recommends: Distributed Archives for Neurophysiology Data Integration recommends: NIDA Data Share recommends: HED Tags lists: University of North Carolina Neuroscience Center and the BRAIN Initiative Viral Vector Core Facility is related to: Brain Image Library is related to: OpenNeuro is related to: Distributed Archives for Neurophysiology Data Integration is related to: NeMO Analytics is related to: Brainome portal is related to: CEMBA MethylC Seq Pipeline is related to: Seattle Alzheimer Disease Brain Cell Atlas is related to: EBRAINS has parent organization: National Institutes of Health is parent organization of: Data Archive BRAIN Initiative is parent organization of: OpenNeuro is parent organization of: Brain Observatory Storage Service and Database (BossDB) is parent organization of: Ecosystem for Multi-modal Brain-behavior Experimentation and Research has organization facet: 3D Developmental Mouse Brain Common Coordinate Framework |
Alzheimer's disease, Schizophrenia, Autism, Epilepsy, Traumatic brain injury | BRAIN Initiative | nlx_155554 | http://braininitiative.nih.gov/ http://www.whitehouse.gov/share/brain-initiative http://en.wikipedia.org/wiki/BRAIN_Initiative |
SCR_006770 | , Brain Research through Advancing Innovative Neurotechnologies Initiative, NIH Brain Research through Advancing Innovative Neurotechnologies Initiative | 2026-02-11 10:57:24 | 18 | |||||
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NCBI Resource List Resource Report Resource Website |
NCBI Resource List (RRID:SCR_005628) | NCBI Resources | organization portal, portal, data or information resource | The National Center for Biotechnology Information''s listing of resources. Sort by alphabetical character, Databases, Downloads, Submissions, Tools and How-To; or by Topic: Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes & Expression; Genetics & Medicine; Genomes & Maps; Homology; Literature; Proteins; Sequence Analysis; Taxonomy; Training & Tutorials; Variation. | database, download, submission, tool, chemical, bioassay, data, software, dna, rna, domain, structure, gene, expression, genetics, medicine, genomes, map, homology, literature, protein, sequence analysis, taxonomy, training, tutorial, variation, gold standard | has parent organization: NCBI | NLM | nlx_146242 | SCR_005628 | NCBI Resource Guide, NCBI Resource List (A-Z) | 2026-02-11 10:57:11 | 0 | |||||||
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Neuroscience Gateway Resource Report Resource Website 10+ mentions |
Neuroscience Gateway (RRID:SCR_008915) | NSG | project portal, portal, software resource, data or information resource | Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists. | Large, scale, modeling, data, computing, neuroscience, neuron, BRAIN Initiative |
is recommended by: BRAIN Initiative lists: ModelRun is related to: XSEDE - Extreme Science and Engineering Discovery Environment is related to: NEURON is related to: GENESIS Neural Database and Modelers Workspace has parent organization: San Diego Supercomputer Center has parent organization: Neuroscience Information Framework has parent organization: Yale School of Medicine; Connecticut; USA |
NSF 1458840; NSF 1458495; BBSRC N005236; NIBIB R01 EB023297; NSF 1339856; NSF 1146949 |
Free, Freely available | nlx_151553, SCR_015767 | http://www.nitrc.org/projects/nsg/ | SCR_008915 | Neuroscience Gateway - A Portal for Computational Neuroscience, Neuroscience Gateway, Neuroscience Gateway (NSG) Portal | 2026-02-11 10:58:03 | 23 | |||||
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Apache Spark Resource Report Resource Website 10+ mentions |
Apache Spark (RRID:SCR_016557) | software resource, software application, data analytics software, data processing software | Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework. | unified, analytics, engine, large, scale, data, processing |
is related to: VariantSpark is related to: spark-xml is related to: spark-xml-utils is related to: SparkFHE has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1145/2934664 | Free, Available for download, Freely available | SCR_016557 | 2026-02-11 10:59:32 | 31 | |||||||||
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Data Biosphere Resource Report Resource Website 1+ mentions |
Data Biosphere (RRID:SCR_016154) | project portal, portal, data or information resource | Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations. | data, environment, biomedicine, standard, module, community | Freely available | https://github.com/databiosphere/ | SCR_016154 | 2026-02-11 10:59:28 | 1 | ||||||||||
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Stanford Center for Reproducible Neuroscience Resource Report Resource Website |
Stanford Center for Reproducible Neuroscience (RRID:SCR_016684) | organization portal, portal, data or information resource | Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects. | computing, tools, neuroscience, data, analyze, reproducibility, fMRI, OpenfMRI, OpenNeuro, Neurovault |
has parent organization: Stanford University; Stanford; California is parent organization of: OpenNeuro is parent organization of: OpenNeuro is parent organization of: NeuroVault |
SCR_016684 | 2026-02-11 10:59:34 | 0 | |||||||||||
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Inxight Resource Report Resource Website 10+ mentions |
Inxight (RRID:SCR_016490) | organization portal, portal, data or information resource, database | Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use. | drug, development, information, approved, marketed, investigational, data, supply, FDA, company, regulatory, status, ingredient, definition, biological, activity, clinical, use | NIH | Free, Freely available | SCR_016490 | 2026-02-11 10:59:30 | 11 | ||||||||||
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NeLS Resource Report Resource Website 1+ mentions |
NeLS (RRID:SCR_016301) | NeLS | organization portal, portal, data or information resource | Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project. | genomic, data, analyze, store, share, archive, electronic, infrastructure, administration, Norway, bio.tools |
is listed by: bio.tools is listed by: Debian |
Research Council of Norway | Free, Freely available | biotools:nels | https://bio.tools/nels https://github.com/elixir-no-nels/nels-core https://bio.tools/nels |
SCR_016301 | Norwegian e-Infrastructure for Life Sciences | 2026-02-11 10:59:29 | 3 | |||||
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hMRI-toolbox Resource Report Resource Website 10+ mentions |
hMRI-toolbox (RRID:SCR_017682) | software resource, software toolkit, software application, data processing software | Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis. | Quantitative, MRI, data, processing, multi, parameter, qMRI, map, spatial, registration, statistical, analysis, histology, longitudinal, relaxation, rate R1 and R2, proton, density, magnetisation, transfer, MT saturation |
is related to: MATLAB is related to: SPM |
European Structural and Investment Fund ; European Regional Development Fund ; Belgian Walloon Government ; European Research Council ; Swiss State Secretariat for Education ; Research and Innovation ; German Research Foundation ; Swiss National Science Foundation ; Leenaards Foundation ; Roger De Spoelberch Foundation ; Wellcome Trust ; Emory Universitys Research Council ; Swedish Research Council |
DOI:10.1016/j.neuroimage.2019.01.029 | Free, Available for download, Freely available | https://github.com/hMRI-group/hMRI-toolbox | SCR_017682 | 2026-02-11 10:59:39 | 33 | |||||||
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BASTA Resource Report Resource Website 1+ mentions |
BASTA (RRID:SCR_017303) | software resource, software application, software toolkit, data processing software | Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations. | Bayesian method, infer, migration, genetic, data, structured, coalescent, approximation, population | is related to: BEAST2 | DOI:10.1371/journal.pgen.1005421 | Free, Available for download, Freely available | SCR_017303 | BAyesian STructured coalescent Approximation, BASTA, BEAST2 | 2026-02-11 10:59:40 | 1 | ||||||||
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Science of Behavior Change Research Network Resource Report Resource Website |
Science of Behavior Change Research Network (RRID:SCR_017385) | SOBC | project portal, portal, data or information resource | Repository for behavioral science measures that have been validated or are in process of being validated in accordance with SOBC Experimental Medicine Approach. | Data, behavioral, science, SOBC, measure, data, medicine | NIH | SCR_017388 | https://scienceofbehaviorchange.org/measures/ https://scienceofbehaviorchange.org/measures/ |
SCR_017385 | SOBC Measures Repository, Science of Behavior Change (SOBC) Research Network | 2026-02-11 10:59:40 | 0 | |||||||
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Allen Human Reference Atlas, 3D, 2020 Resource Report Resource Website 1+ mentions |
Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) | atlas, reference atlas, data or information resource | Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas. | Parcellation, adult, human, brain, 3D, atlas, data |
is used by: BICCN has parent organization: Allen Institute |
Allen Institute for Brain Science ; NIMH U01 MH114812 |
Free, Available for download, Freely available | SCR_017764 | 2026-02-11 10:59:45 | 3 | |||||||||
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Mnemiopsis Genome Project Portal Resource Report Resource Website |
Mnemiopsis Genome Project Portal (RRID:SCR_018293) | MGP Portal | project portal, portal, data or information resource | Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis. | Genomic, data, metazoan development, Mnemiopsis leidyi, Ctenophore, moel organisms, genomic data analysis |
is related to: University of Michigan; Ann Arbor; USA is related to: Brown University; Rhode Island; USA is related to: University of Florida; Florida; USA |
Free, Freely available | SCR_018293 | 2026-02-11 10:59:46 | 0 | |||||||||
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Hierarchical Data Modeling Framework Resource Report Resource Website 1+ mentions |
Hierarchical Data Modeling Framework (RRID:SCR_021303) | HDMF | software resource, software toolkit, software application, data processing software | Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data. | Hierarchical data, data models, reading data, writing data, unified data format, different storage backends, Python object, data, data standards |
is used by: PyNWB is related to: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Documentation Utilities is related to: HDMF Common Schema |
DOI:10.1109/BigData47090.2019.9005648 | Free, Available for download, Freely available | SCR_021303 | 2026-02-11 11:00:05 | 1 |
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