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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RIPPLELAB Resource Report Resource Website 10+ mentions |
RIPPLELAB (RRID:SCR_015876) | data processing software, data visualization software, software application, software resource, source code | Source code for processing continuous local field potentials (LFP). The interface implements different documented algorithms for HFO detection, and provides several tools for signal visualization and manipulation. | lfp, local field potential, continuous local field potential, computing platform | Free, Available for download | SCR_015876 | SciCrunch Registry | RIPPLELAB Multi Analysis EEG Project | 2026-10-17 01:29:05 | 16 | ||||||||||
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NiftyPET Resource Report Resource Website 1+ mentions |
NiftyPET (RRID:SCR_015873) | data processing software, data visualization software, image analysis software, software application, software resource, software toolkit, source code | Python software package that offers quantitative PET image reconstruction and analysis with high accuracy and precision. It is written in CUDA C and embedded in Python C extensions. | python, cuda c, python c, pet, image reconstruction, image analysis, bio.tools |
uses: CMake is listed by: Debian is listed by: bio.tools |
DOI:10.1007/s12021-017-9352-y | Free, Available for download, Runs on Windows, Runs on Linux | biotools:niftypet | https://bio.tools/niftypet | SCR_015873 | SciCrunch Registry | 2026-10-17 01:29:17 | 7 | |||||||
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Perseus Resource Report Resource Website 1000+ mentions |
Perseus (RRID:SCR_015753) | data analysis software, data processing software, software application, software resource | Software that supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiplehypothesis testing. | shotgun proteomics data analysis, protein quantification, post-translational modification data, statistical analysis, omics data | European Union 686547; European Union GA ERC-2012-SyG_318987–ToPAG |
PMID:27348712 | Free, Available for download, Runs on Windows, Runs on Mac OS, Tutorial available, Account required | http://www.biochem.mpg.de/5111810/perseus | SCR_015753 | SciCrunch Registry | 2026-10-17 01:29:03 | 4024 | ||||||||
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BECA Resource Report Resource Website 1+ mentions |
BECA (RRID:SCR_015846) | BECA | data processing software, data visualization software, image analysis software, software application, software resource | 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 | NIA P30 AG10133; NIA R01 AG19771; NIA RC2 AG036535; NIA U01 AG024904; NIBIB R01 EB022574; NLM R01 LM011360; NSF IIS-1117335 |
PMID:27171688 | Free, Available for download | SCR_015846 | SciCrunch Registry | Brain Explorer for Connectome Analysis (BECA), BECA - Brain Explorer for Connectome Analysis | 2026-10-17 01:29:05 | 5 | ||||||
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Alliance of Genome Resources Resource Report Resource Website 50+ mentions |
Alliance of Genome Resources (RRID:SCR_015850) | access service resource, consortium, data or information resource, organization portal, portal, service resource | 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 | SciCrunch Registry | The Alliance | 2026-10-17 01:29:17 | 87 | |||||||||
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funRiceGenes Resource Report Resource Website 50+ mentions |
funRiceGenes (RRID:SCR_015778) | data or information resource, data set, database | 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 | SciCrunch Registry | RICENCODE | 2026-10-17 01:29:15 | 53 | ||||||||
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Leica HCS A Resource Report Resource Website 1+ mentions |
Leica HCS A (RRID:SCR_015811) | data acquisition software, data processing software, image acquisition software, image processing software, software application, software resource | 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 | SciCrunch Registry | Leica High Content Screening Automation, High Content Screening Automation Leica HCS A | 2026-10-17 01:29:01 | 1 | ||||||||||
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Cross-species scaffolding Resource Report Resource Website 1+ mentions |
Cross-species scaffolding (RRID:SCR_015932) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | 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 | SciCrunch Registry | cross-species-scaffolding | 2026-10-17 01:29:02 | 1 | |||||||||
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Dat Project Resource Report Resource Website 1+ mentions |
Dat Project (RRID:SCR_015779) | community building portal, data or information resource, data repository, database, portal, protocol, service resource, storage service resource | 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 | SciCrunch Registry | The Dat Project, datproject.org, Dat Protocol, Dat | 2026-10-17 01:28:57 | 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 | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit, source code | 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 | SciCrunch Registry | End Sequence Analysis ToolKit | 2026-10-17 01:29:16 | 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 | SciCrunch Registry | 2026-10-17 01:28:58 | 7 | |||||||||||
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MicrobeTracker Resource Report Resource Website 100+ mentions |
MicrobeTracker (RRID:SCR_015939) | data processing software, image analysis software, software application, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them. | microbe, tracking, tracker, matlab, microscopy, microbiology, bacteria, cell, cell imaging, imaging, image, analysis |
uses: MATLAB requires: MATLAB |
SCR_015939 | SciCrunch Registry | 2026-10-17 01:29:05 | 119 | |||||||||||
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larvalign Resource Report Resource Website 1+ mentions |
larvalign (RRID:SCR_015815) | data analysis software, data or information resource, data processing software, data set, sequence analysis software, software application, software resource, software toolkit | 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 | SciCrunch Registry | 2026-10-17 01:29:01 | 1 | ||||||||
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CluePedia Cytoscape plugin Resource Report Resource Website 100+ mentions |
CluePedia Cytoscape plugin (RRID:SCR_015784) | data analysis software, data processing software, data visualization software, software application, software resource | 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 | SciCrunch Registry | CluePedia: A ClueGO plugin, CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data | 2026-10-17 01:29:15 | 193 | |||||||
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Flowing Software 2.5.1 Resource Report Resource Website 100+ mentions |
Flowing Software 2.5.1 (RRID:SCR_015781) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | Flowing Software | 2026-10-17 01:29:01 | 134 | |||||||||
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BICCN Resource Report Resource Website 100+ mentions |
BICCN (RRID:SCR_015820) | BICCN | consortium, data or information resource, organization portal, 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 has organization facet: Smart-seq2 Multi-Sample Pipeline |
NIMH U19 MH114821; NIMH U19 MH114830; NIMH U19 MH114831 |
PMID:37390046 | Restricted | SCR_017266 | SCR_015820 | SciCrunch Registry | BICCN 2.0, BRAIN Initiative Cell Census Network, BRAIN Initiative Cell Census Network (BICCN) | 2026-10-17 01:29:04 | 234 | |||||
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Piggy Resource Report Resource Website 10+ mentions |
Piggy (RRID:SCR_015941) | data analysis software, data processing software, software application, software resource | Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary). | intergenic, region, bacterial, analysis, gene, genome, assembly | Medical Research Council | Free, Available for download | SCR_015941 | SciCrunch Registry | 2026-10-17 01:29:02 | 32 | ||||||||||
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Feeding Experimentation Device project Resource Report Resource Website 1+ mentions |
Feeding Experimentation Device project (RRID:SCR_015942) | FED | data or information resource, portal, topical portal | Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging. | Feeding, food intake, optogenetic, behavioral data analysis, data analysis software, behavior apparatus, behavior rig, reward delivery, behavior measurement, homecage, Instrument, OpenBehavior |
is listed by: OpenBehavior has parent organization: Washington University in St. Louis; Missouri; USA |
NIH | PMID:27060385 | Commercially available | https://github.com/KravitzLab/FED1, https://edspace.american.edu/openbehavior/project/feeding-experimentation-device/, https://hackaday.io/project/72964-feeding-experimentation-device-fed-20 | SCR_015942 | SciCrunch Registry | , FED1, FED2, Feeding Experimentation Device system, Feeding Experimentation Device | 2026-10-17 01:29:18 | 1 | |||||
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BeatBox Resource Report Resource Website 10+ mentions |
BeatBox (RRID:SCR_015780) | simulation software, software application, software resource | 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 | SciCrunch Registry | BeatBox—HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology. | 2026-10-17 01:29:04 | 11 | |||||||
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BioVoxxel Toolbox Resource Report Resource Website 10+ mentions |
BioVoxxel Toolbox (RRID:SCR_015825) | data processing software, image analysis software, software application, software resource, software toolkit | 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 | SciCrunch Registry | BioVoxxel, BioVoxxel Toolbox (ImageJ/Fiji) | 2026-10-17 01:29:04 | 33 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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