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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BECA Resource Report Resource Website 1+ mentions |
BECA (RRID:SCR_015846) | BECA | image analysis software, software resource, software application, data visualization software, data processing software | Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version. | visual exploration, brain, neuroscience, network, genetic determinant, fmri, neuroimaging, genome | has parent organization: Indiana University School of Medicine; Indiana; USA | NLM R01 LM011360; NIA U01 AG024904; NIA RC2 AG036535; NIA R01 AG19771; NIA P30 AG10133; NSF IIS-1117335; NIBIB R01 EB022574 |
PMID:27171688 | Free, Available for download | SCR_015846 | Brain Explorer for Connectome Analysis (BECA), BECA - Brain Explorer for Connectome Analysis | 2026-08-08 12:00:42 | 5 | ||||||
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Alliance of Genome Resources Resource Report Resource Website 50+ mentions |
Alliance of Genome Resources (RRID:SCR_015850) | data or information resource, access service resource, consortium, service resource, portal, organization portal | Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN). | gene ontology, human biology, genome, organism model, gene ontology consortium, FASEB list, DRKB |
has organization facet: WormBase has organization facet: Mouse Genome Databases has organization facet: FlyBase has organization facet: Gene Ontology has organization facet: SGD has organization facet: Rat Genome Database (RGD) has organization facet: Zebrafish Information Network (ZFIN) |
NHGRI U41HG02223E; NIH HG010859 |
SCR_015850 | The Alliance | 2026-08-08 12:00:26 | 87 | |||||||||
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funRiceGenes Resource Report Resource Website 50+ mentions |
funRiceGenes (RRID:SCR_015778) | database, data or information resource, data set | Dataset of functionally characterized rice genes and members of different gene families. The dataset was created by integrating data from available databases and reviewing publications of rice functional genomic studies. | rice, functional genomics, interaction network, genetic improvement, gene, data integration | National Key Research and Development Program of China 2016YFD0100903; National Natural Science Foundation of China 31771873 and National Natural Science Foundation of China; Outstanding Young Talents Program |
Freely available, Public, Available for download, Free | https://github.com/venyao/RICENCODE, http://funricegenes.ncpgr.cn/ | SCR_015778 | RICENCODE | 2026-08-08 12:00:44 | 53 | ||||||||
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Leica HCS A Resource Report Resource Website 1+ mentions |
Leica HCS A (RRID:SCR_015811) | image acquisition software, image processing software, data acquisition software, software resource, software application, data processing software | Software supporting Leica Microsystem microscopes by performing high content screening automation. The software combines the flexibility of a point-scanning confocal with the high speed of a camera-based widefield system to compensate for specimen drift, single object tracking and immersion fluid. | high content screening automation, automation, confocal, widefield, microscope, leica | Commercially available, Available for purchase, Demo available | SCR_015811 | Leica High Content Screening Automation, High Content Screening Automation Leica HCS A | 2026-08-08 12:00:42 | 1 | ||||||||||
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Cross-species scaffolding Resource Report Resource Website 1+ mentions |
Cross-species scaffolding (RRID:SCR_015932) | sequence analysis software, software resource, software application, source code, data analysis software, data processing software | Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references. | mate, pair, end, reference, genome | Free, Available for download, Freely available | SCR_016125 | SCR_015932 | cross-species-scaffolding | 2026-08-08 12:00:46 | 1 | |||||||||
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Dat Project Resource Report Resource Website 1+ mentions |
Dat Project (RRID:SCR_015779) | data or information resource, community building portal, protocol, database, service resource, storage service resource, portal, data repository | Community portal for a distributed data sharing platform and open protocol for building apps. The Dat Project imagines a web of commons created by global communities on open and secure protocols. | data sharing, collaborative work | Knight Foundation ; Alfred P. Sloan Foundation |
Open Source, Freely available | SCR_015779 | The Dat Project, datproject.org, Dat Protocol, Dat | 2026-08-08 12:00:26 | 2 | |||||||||
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End Sequence Analysis ToolKit (ESAT) Resource Report Resource Website 1+ mentions Rating or validation data |
End Sequence Analysis ToolKit (ESAT) (RRID:SCR_015812) | ESAT | sequence analysis software, software toolkit, software resource, software application, source code, data analysis software, data processing software | Software for the analysis of short reads obtained from end-sequence RNA-seq. ESAT is designed for expression analysis of Digital expression (DGE) libraries that target transcript "ends." | short read, rna-seq, expression analysis, dge, digital expression library, transcript end, sequence analysis, alignment, sam file, bam file | PMID:27470110 | Free, Available for download | SCR_015812 | End Sequence Analysis ToolKit | 2026-08-08 12:00:44 | 9 | ||||||||
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Neuroscan SynAmps RT 64-channel Amplifier Resource Report Resource Website 1+ mentions |
Neuroscan SynAmps RT 64-channel Amplifier (RRID:SCR_015818) | resource | Equipment that is an EEG signal amplifier for 64-channel montages. It is suitable for recording data from high sampling rate (20,000 Hz) Auditory Brain Stem recordings and Spike Spindles to true DC recordings of CNV and P300. | eeg, signal amplifier, signal amplification, 64 channel, neuroimaging, hardware, instrument, equipment | Commercially available, Available for purchase | SCR_015818 | 2026-08-08 12:00:42 | 7 | |||||||||||
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larvalign Resource Report Resource Website 1+ mentions |
larvalign (RRID:SCR_015815) | sequence analysis software, data or information resource, software toolkit, software resource, software application, data set, data analysis software, data processing software | Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping. | drosophila melanogaster, computational method, gene expression, alignment, larval brain, larvae, template generation, mapping, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download | biotools:larvalign | https://bio.tools/larvalign | SCR_015815 | 2026-08-08 12:00:44 | 1 | ||||||||
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CluePedia Cytoscape plugin Resource Report Resource Website 100+ mentions |
CluePedia Cytoscape plugin (RRID:SCR_015784) | software resource, software application, data analysis software, data visualization software, data processing software | Data analysis software and search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data and investigates interrelations within each pathway to reveal associations through gene/protein/miRNA enrichments. | cytoscape, cluepedia, search tool, marker, pathway, experimental data, in silico data, linear dependence, gene, protein, miRNA | is a plug in for: Cytoscape | INCa ; Canceropole Ile de France ; INSERM ; MedImmune ; Qatar National Research Fund NPRP09-1174-3-291; European Commission 7FP Geninca 202230); LabEx Immuno-Oncology |
PMID:23325622 | Free for non-profits, Free for academic use, Available for download, Commercially available, Available for purchase | SCR_015784 | CluePedia: A ClueGO plugin, CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data | 2026-08-08 12:00:26 | 193 | |||||||
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Flowing Software 2.5.1 Resource Report Resource Website 100+ mentions |
Flowing Software 2.5.1 (RRID:SCR_015781) | software resource, software application, data analysis software, data processing software | Software for flow cytometry data analysis. Flowing Software has many common analysis tools, such as dot plots, histograms, quadrants, statistics, overlay histograms etc. | cytometry, flow cytometry, flow cytometry data, data analysis, box plot, histogram, quadrant, statistic, overlay histogram | Free, Available for download | http://www.flowingsoftware.com/, https://en.freedownloadmanager.org/users-choice/Flowing_Software_2.5.1.html | SCR_015781 | Flowing Software | 2026-08-08 12:00:44 | 134 | |||||||||
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BICCN Resource Report Resource Website 100+ mentions |
BICCN (RRID:SCR_015820) | BICCN | portal, data or information resource, consortium, organization portal | Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains. | cell census, neuroscience, brain, brain initiative cell census network, whole mouse brain, |
uses: QuickNII uses: HistoloZee uses: CellLocator uses: Semi-Manual Alignment to Reference Templates uses: LoomPy uses: Cytosplore Viewer uses: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) uses: Blue Brain Cell Atlas uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Hippocampome.org uses: Neuron Phenotype Ontology uses: Brain Image Library uses: Distributed Archives for Neurophysiology Data Integration uses: NeuroMorpho.Org uses: Azimuth uses: Brain Observatory Storage Service and Database (BossDB) uses: Optimus Pipeline uses: scATAC Pipeline uses: Smart-seq2 Single Nucleus Multi Sample Pipeline uses: CEMBA MethylC Seq Pipeline uses: Brain Architecture Project uses: Single Cell Portal uses: MorphoHub uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Mouse Connectome Project uses: Allen Mouse Brain Reference Atlas uses: Allen Mouse Brain Common Coordinate Framework uses: Allen Human Reference Atlas, 3D, 2020 uses: NeMO Analytics uses: ANTS - Advanced Normalization ToolS uses: CloudReg uses: Brainome portal uses: CATlas uses: MetaNeighbor uses: Cell Annotation Platform uses: cellxgene uses: Neuroglancer uses: Vaa3D uses: QuickNII and VisuAlign uses: Hi5App uses: CloudVolume uses: neuroXiv uses: Brain Data Standards Ontology uses: Pittsburgh Supercomputing Center uses: Molecular Biosensor and Imaging Center uses: Generative Diffeomorphic Mapping uses: NIH NeuroBioBank uses: NeMOarchive lists: ccf_streamlines is related to: Mouse Connectome Project is related to: BarensLab Mini-Atlas is related to: Cumulus is related to: Pegasus is related to: Cirrocumulus is related to: Gene functional conservation across cell types and species is related to: BRAIN Initiative Cell Atlas Network is related to: ATAC Pipeline is related to: Slide-seq Pipeline is related to: Brain Knowledge Platform has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science provides: mBrainAligner provides: BICCN Cell Registry provides: Cell Type Knowledge Explorer provides: Epiviz has organization facet: BICCN Anatomy and Morphology Project has organization facet: Cell Type Knowledge Explorer has organization facet: mBrainAligner has organization facet: Terra has organization facet: Allen Brain Cell Atlas has organization facet: Multiome Pipeline has organization facet: Allen Software Development Kit has organization facet: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain has organization facet: Allen Brain Map BICCN Data Catalog has organization facet: snm3C Pipeline has organization facet: Paired-Tag Pipeline has organization facet: BuildIndices has organization facet: MapMyCells |
NIMH U19 MH114821; NIMH U19 MH114830; NIMH U19 MH114831 |
PMID:37390046 | Restricted | SCR_017266 | SCR_015820 | BICCN 2.0, BRAIN Initiative Cell Census Network, BRAIN Initiative Cell Census Network (BICCN) | 2026-08-08 12:00:44 | 234 | |||||
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BeatBox Resource Report Resource Website 10+ mentions |
BeatBox (RRID:SCR_015780) | software resource, software application, simulation software | Simulation environment that combines flexible script language user interface with computational tools in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level. It aims to include cell excitation, tissue/anatomy models, and stimulation protocols in BeatBox scripts so that simulation run either sequentially or in parallel (MPI) without re-compilation. | simulation, cardiac electrophysiology, computation, script language, c, ecg, heart, cardiology, simulation protocol | EPSRC EP/I029664; EPSRC EP/N014391/1; EPSRC EP/P008690/1 |
PMID:28467407 | Free, Available for download | https://github.com/beatbox-heart/beatbox-public/tree/v1.7.982 | SCR_015780 | BeatBox—HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology. | 2026-08-08 12:00:41 | 11 | |||||||
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BioVoxxel Toolbox Resource Report Resource Website 10+ mentions |
BioVoxxel Toolbox (RRID:SCR_015825) | software toolkit, image analysis software, software resource, software application, data processing software | Software toolkit for analyzing tool for microscopic images. It contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis. | microscopic image analysis, image filtering, image segmentation, binary processing, binary analysis, particle analysis |
is related to: ImageJ is a plug in for: ImageJ is a plug in for: Fiji/ImageJ is a plug in for: Fiji |
Free, Available for download | https://imagej.net/BioVoxxel_Toolbox, https://github.com/biovoxxel/BioVoxxel_Toolbox | SCR_015825 | BioVoxxel, BioVoxxel Toolbox (ImageJ/Fiji) | 2026-08-08 12:00:26 | 33 | ||||||||
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DiPDE Resource Report Resource Website 1+ mentions |
DiPDE (RRID:SCR_015822) | software resource, software application, source code, simulation software, data analysis software, data processing software | Simulation platform for numerically solving the time evolution of coupled networks of neuronal populations. DiPDE can facilitate the fast exploration of mesoscale (population-level) network topologies, where large populations of neurons are treated as homogeneous with random fine-scale connectivity. | simulation, time evolution, coupled network, neuron population, neural network, mesoscale network topology, fine-scale connectivity | Allen Institute for Brain Science | Free, Available for download | https://github.com/AllenInstitute/dipde | SCR_015822 | DiPDE (Integro-partial differential equation with displacement), dipde | 2026-08-08 12:00:42 | 3 | ||||||||
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FiberApp Resource Report Resource Website 10+ mentions |
FiberApp (RRID:SCR_015826) | software resource, software application, data analysis software, data processing software | Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects. | semiflexible polymer, neurodegenerative disease, fiber-like object, topography, tracking, analysis, microscopic image analysis | Swiss National Science Foundation SNF 2-77002-11 | Open source, Available for download | SCR_015826 | FiberApp: An Open-Source Software for Tracking and Analyzing Polymers, Biomacromolecules, Filaments, and Fibrous Objects | 2026-08-08 12:00:42 | 28 | |||||||||
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LI-COR Image Studio Software Resource Report Resource Website 100+ mentions |
LI-COR Image Studio Software (RRID:SCR_015795) | image analysis software, data acquisition software, software resource, software application, data processing software | Image analysis software that acquires, analyzes, and archives research data without altering raw findings. It integrates data and changes how pixels are mapped to the screen for clearer display, rather than altering the pixels of the image data itself. | image studio, image analysis, raw data, image acquisition, pixel mapping, image viewer | Commercially available, Available for purchase, Free version available, Runs on Windows, Runs on MAC OS | https://www.licor.com/bio/products/software/image_studio | SCR_015795 | LI-COR Image Studio, Image Studio™ Software | 2026-08-08 12:00:42 | 223 | |||||||||
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Sigma: Millicell Cell Culture Inserts Resource Report Resource Website 10+ mentions |
Sigma: Millicell Cell Culture Inserts (RRID:SCR_015799) | instrument resource | Equipment that provides physical support for cell cultures. These cell culture inserts feature attachment and suspension cells that can access media from both their apical and basolateral sides. | cell culture, culture insert, hardware, attachment, suspension cell, apical side, basolateral side, instrument, equipment | Commercially available, Available for purchase | https://drive.google.com/file/d/1iKvbwq8VXv1PtD0ItetDiDk8tUv0RwlR/view?usp=drivesdk | https://www.emdmillipore.com/US/en/product/Millicell-Cell-Culture-Inserts, MM_NF-C10504?amp%3Bbd=1&bd=1#documentation | http://www.merckmillipore.com/ES/es/product/Millicell-Cell-Culture-Inserts, MM_NF-C10504?ReferrerURL=https%3A%2F%2Fwww.google.es%2F&bd=1 | SCR_015799 | Millicell® Cell Culture Inserts | 2026-08-08 12:00:44 | 10 | |||||||
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Adobe Audition Resource Report Resource Website 1+ mentions |
Adobe Audition (RRID:SCR_015796) | authoring tool, software toolkit, software resource, software application, data analysis software, data processing software | Software for sound analysis, audio editing, and audio recording. It features multitrack, waveform, and spectral display for creating, mixing, editing, and restoring audio content for research or non-research purposes. | audio, editing, recording, sound analysis, audio analysis, audio editing, adobe | Commercially available, Available for purchase | SCR_015796 | Adobe Audition CC | 2026-08-08 12:00:44 | 8 | ||||||||||
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NAPR: Neuroanatomical Age Prediction using R Resource Report Resource Website 1+ mentions |
NAPR: Neuroanatomical Age Prediction using R (RRID:SCR_015759) | NAPR | storage service resource, data repository, service resource | Cloud-based framework that allows users to estimate the age of individual subjects using cortical thickness maps derived from their own locally processed T1-weighted whole brain MRI scans. The provided age prediction models were trained using (i) relevance vector machines and (ii) Gaussian processes machine learning methods applied to cortical thickness surfaces obtained using Freesurfer v5.3. | neuroanatomy, prediction, r, neuroimaging, mri scan, cortical thickness, relevance vector | DOI:10.1101/099309 | Free, Available for download | http://www.cloudneuro.org/ | SCR_015759 | Neuroanatomical Age Prediction using R | 2026-08-08 12:00:25 | 1 |
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