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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ChromHMM Resource Report Resource Website 10+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, software resource, data processing software, software application | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
NHGRI U54 HG004570; NHGRI RC1HG005334; NIEHS R01 ES024995; NHGRI U01 HG007912; NIMH U01 MH105578; NSF 0905968; Alfred P. Sloan Fellowship ; CAREER Award |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-02-14 02:03:27 | 47 | ||||||
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Track-A-Worm Resource Report Resource Website 1+ mentions |
Track-A-Worm (RRID:SCR_018299) | data analysis software, software resource, data processing software, software application | Open source system for quantitative assessment of C. Elegans locomotory and bending behavior. Used for quantitative behavioral analyses to understand circuit and gene bases of behavior. Constantly records and analyzes position and body shape of freely moving worm at high magnification. | Quantitative assessment, C.Elegans locomotory, bending behavior, behavioral analysis, gene, moving worm position, body shape, automated recording | is related to: University of Connecticut; Connecticut; USA | NIGMS R01 GM083049; NIMH R01 MH085927 |
PMID:23922769 | Free, Available for download, Freely available | SCR_018299 | Tracker-A-Worm version 1.0, Tracker-A-Worm version 2.0 | 2026-02-14 02:03:30 | 3 | |||||||
|
EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | data processing software, data analysis software, software toolkit, software application, software resource | Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. | Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools |
is listed by: Debian is listed by: bio.tools |
NICHD R01 HD068395; NIMH R21 MH112449; NICHD R21 HD075662; NIDA P30 DA027828; NIAID P30 AI050409; NIAID P30 AI027757; NICHD T32 HD007543 |
PMID:29731699 | Free, Available for download, Freely available | biotools:epimodel | https://bio.tools/epimodel | SCR_018539 | 2026-02-14 02:03:34 | 7 | ||||||
|
piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NHLBI U54 HL127624; NIEHS P30 ES006096; NIMH R01 MH107487; NCI T32 CA236764; NCATS UL1 TR001425; NIGMS U01 GM120953 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-02-14 02:03:42 | 4 | ||||||||
|
Scalable Analytics for Brain Exploration Research Resource Report Resource Website 1+ mentions |
Scalable Analytics for Brain Exploration Research (RRID:SCR_018812) | SABER, saber | data processing software, software library, workflow software, software toolkit, software application, software resource | Library of containerized tools and workflow deployment system for enabling processing of large neuroimaging datasets. Provides canonical neuroimaging workflows specified in standard workflow language (CWL), integration with workflow execution engine (Airflow), imaging database (bossDB), and parameter database (Datajoint) to deploy workflows at scale, and tools to automate deployment and optimization of neuroimaging pipelines. | Running containerized workflow, large neuroimaging datasets, canonical neuroimaging workflow, neuroimaging pipeline deployment, neuroimaging pipeline optimization | is related to: Brain Observatory Storage Service and Database (BossDB) | NIMH R24 MH114799 | DOI:10.1101/615161v1.full | Free, Available for download, Freely available | SCR_018812 | 2026-02-14 02:03:41 | 1 | |||||||
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RAVE Resource Report Resource Website 1+ mentions |
RAVE (RRID:SCR_019040) | data visualization software, data processing software, data analysis software, software application, software resource | Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG). | Intracranial EEG data, data analysis, intracranial electroencephalogram data, electrocorticography data, depth electrodes, stereotactic EEG, iEEG data | NIMH R24 MH117529 | DOI:10.1016/j.neuroimage.2020.117341 | Free, Available for download, Freely available | SCR_019040 | R Analysis and Visualization of intracranial EEG | 2026-02-14 02:03:45 | 1 | ||||||||
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Pulse Pal Resource Report Resource Website 1+ mentions |
Pulse Pal (RRID:SCR_017203) | instrument resource | Open source pulse train generator that allows users to create and trigger software defined trains of voltage pulses with high temporal precision. Generates precisely timed pulse sequences for use in research involving electrophysiology or psychophysics. | instrument, generator, stimulation, voltage, puls, sequence, electrophysiology, psychophysics | NINDS R01 NS07553; NIMH R01 MH097061; McKnight Foundation |
DOI:10.3389/fneng.2014.00043 | Available for purchase | https://sanworks.io/shop/viewproduct?productID=1102 https://github.com/sanworks/PulsePal https://sites.google.com/site/pulsepalwiki/specifications?authuser=0 |
SCR_017203 | Pulse Pal v2 | 2026-02-14 02:03:16 | 1 | |||||||
|
PIVOT software Resource Report Resource Website 10+ mentions |
PIVOT software (RRID:SCR_017210) | PIVOT | data analysis software, software resource, data processing software, software application | Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows. | Interactive, analysis, visualization, transcriptomics, data | is related to: University of Pennsylvania; Philadelphia; USA | NIMH U01 MH098953 | PMID:29304726 | Free, Available for download, Freely available | SCR_017210 | Platform for Interactive analysis and Visualization Of Transcriptomics, PIVOT, KimLabIDV | 2026-02-14 02:03:25 | 17 | ||||||
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Neuron Phenotype Ontology Resource Report Resource Website 1+ mentions |
Neuron Phenotype Ontology (RRID:SCR_017403) | NPO | data or information resource, ontology, controlled vocabulary | An ontology for describing the complex phenotypes of neurons. | Cell, type, phenotype, neuron, ontology |
is used by: BICCN is provided by: NIFSTD |
NIMH U24 MH114827; BRAIN Initiative |
Free, Freely available | SCR_017403 | 2026-02-14 02:03:12 | 2 | ||||||||
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Brain Image Library Resource Report Resource Website 10+ mentions |
Brain Image Library (RRID:SCR_017272) | BIL | data or information resource, data repository, storage service resource, service resource | Repository for confocal microscopy brain imaging data. Data archives that have been established by BRAIN Initiative Data Sharing. National public resource enabling researchers to deposit, analyze, mine, share and interact with large brain image datasets. Operated as partnership between Biomedical Applications Group at Pittsburgh Supercomputing Center, Center for Biological Imaging at University of Pittsburgh and Molecular Biosensor and Imaging Center at Carnegie Mellon University. Provides persistent centralized repository for brain microscopy data. | archive, dataset, confocal, microscopy, brain, image, data, brain microscopy data, |
is used by: BICCN is used by: BRAIN Initiative Cell Atlas Network is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is listed by: DataCite is listed by: re3data.org is related to: BRAIN Initiative is related to: Allen Institute for Brain Science works with: CBI BrAinPI is organization facet of: BRAIN Initiative Cell Atlas Network |
BRAIN Initiative ; NIMH R24 MH114793 |
PMID:38187527 | Free, Available for download, Freely available | DOI:10.17616/R31NJN9G, DOI:10.35077, r3d100013956 | https://doi.org/10.17616/R31NJN9G https://doi.org/10.17616/r31NJN9G https://doi.org/10.35077/ https://dx.doi.org/10.35077/ https://doi.org/10.17616/R31NJN9G |
SCR_017272 | Brain Image Library | 2026-02-14 02:03:17 | 16 | ||||
|
Brain Observatory Storage Service and Database (BossDB) Resource Report Resource Website 10+ mentions |
Brain Observatory Storage Service and Database (BossDB) (RRID:SCR_017273) | BossDB, bossDB, BOSS DB | data repository, storage service resource, 3d spatial image, data or information resource, service resource, image, database | BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest. | Johns Hopkins University Applied Physics Laboratory, JHU/APL, database, electron microscopy, xray, data, storage, archive, BRAIN Initiative, EM, XRM, XNH, ecosystem |
is used by: BICCN is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is related to: Scalable Analytics for Brain Exploration Research is related to: Ecosystem for Multi-modal Brain-behavior Experimentation and Research has parent organization: BRAIN Initiative has parent organization: Johns Hopkins University; Maryland; USA |
BRAIN Initiative ; NIMH R24 MH114785 |
DOI:10.1101/217745 | Open | https://github.com/jhuapl-boss/boss/ | SCR_017273 | Brain Observatory Storage Service, bossDB, Block and Object Storage Service, BOSSDB, Block and Object Storage Service Database, Brain Observatory Storage Service and Database, BossDB | 2026-02-14 02:03:26 | 27 | |||||
|
gene Expression Analysis Resource Resource Report Resource Website 50+ mentions |
gene Expression Analysis Resource (RRID:SCR_017467) | gEAR | portal, analysis service resource, data or information resource, production service resource, service resource, software resource | Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data. | Visualization, analysis, multi, omic, data, upload, scRNA-seq, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Maryland School of Medicine; Maryland; USA |
NIMH MH114788; NIDCD R01 DC013817; NIMH R24 MH114815; Hearing Health Foundation (Hearing Restoration Project) |
Restricted | SCR_017467 | gene Expression Analysis Resource | 2026-02-14 02:03:20 | 76 | |||||||
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TReNA Resource Report Resource Website |
TReNA (RRID:SCR_017458) | network analysis software, data processing software, data analysis software, software application, software resource | Methods for reconstructing transcriptional regulatory networks. | Reconstructing, transcriptional, regulatory, network, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH114788 | Free, Available for download, Freely available | SCR_017458 | 2026-02-14 02:03:28 | 0 | |||||||||
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SnapATAC Resource Report Resource Website 10+ mentions |
SnapATAC (RRID:SCR_020981) | data processing software, data analysis software, software toolkit, software application, software resource | Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset. | scATAC-seq datasets analysis, dissects cellular heterogeneity, cellular states, map trajectories | NCI K99 CA252020; UCSD School of Medicine ; NIMH U19 MH114831 |
PMID:33637727 | Free, Available for download, Freely available | https://github.com/r3fang/SnapATAC | SCR_020981 | Single Nucleus Analysis Pipeline for ATAC-seq | 2026-02-14 02:04:35 | 22 | |||||||
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LeafCutter Resource Report Resource Website 10+ mentions |
LeafCutter (RRID:SCR_017639) | data processing software, data analysis software, data analytics software, software application, software resource | Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs). | Identify, quantitate, RNA, splicing, variation, intron, short, read, RNAseq, data, mapping, trait, loci, sQTL | has parent organization: Stanford University; Stanford; California | CEHG Fellowship ; Howard Hughes Medical Institute ; NHGRI HG007036; NHGRI HG008140; NHGRI HG009431; NIMH R01 MH107666 |
PMID:29229983 DOI:10.1038/s41588-017-0004-9 |
Free, Available for download, Freely available | SCR_017639 | 2026-02-14 02:04:39 | 29 | ||||||||
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Vocal Inventory Clustering Engine (VoICE) Resource Report Resource Website 1+ mentions |
Vocal Inventory Clustering Engine (VoICE) (RRID:SCR_016004) | VoICE | data analysis software, software resource, data processing software, software application | Software that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations. | bird, song, birdsong, vocal, audio, analysis, vocalization, spectral similarity, avian, matlab | uses: MATLAB | Autism Speaks 7657; UCLA ; 5T32HC00722834 ; NIMH RO1MH081754; NICHD P50 HD055784; NIMH R01 MH081754; NIMH R01 MH070712 |
Free, Available for download | SCR_016004 | VoICE (Vocal Inventory Clustering Engine), Vocal Inventory Clustering Engine (VoICE), VoICE: Vocal Inventory Clustering Engine, VoICE: A semi-automated pipeline for standardizing vocal analysis across models | 2026-02-14 02:04:37 | 1 | |||||||
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Drop-seq tools Resource Report Resource Website 50+ mentions |
Drop-seq tools (RRID:SCR_018142) | data analysis software, software resource, data processing software, software application | Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript. | Simultaneous analysis, Drop-seq data, gene expression, thousands individual cells |
is listed by: Debian has parent organization: Broad Institute |
Stanley Center for Psychiatric Research ; MGH Psychiatry Residency Research Program ; Stanley-MGH Fellowship in Psychiatric Neuroscience ; Stewart Trust Fellows Award ; Simons Foundation ; NHGRI P50 HG006193; Klarman Cell Observatory ; NIMH U01 MH105960; NIMH R25 MH094612; NICHD F32 HD075541; NSF ECS 0335765; NSF DMR 1310266; NSF DMR 1420570 |
PMID:26000488 | https://sources.debian.org/src/drop-seq-tools/ | SCR_018142 | Droplet sequencing tools, Droplet sequencing data analysis software tools | 2026-02-14 02:04:35 | 94 | |||||||
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Open Access Series of Imaging Studies Resource Report Resource Website 100+ mentions |
Open Access Series of Imaging Studies (RRID:SCR_007385) | OASIS | data or information resource, database | Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated. | early, stage, alzheimer, disease, mri, fmri, image, brain, dicom, magnetic, resonance, collection, data, FASEB list |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Automatic Registration Toolbox is related to: 2012 MICCAI Multi-Atlas Labeling Challenge Data has parent organization: Howard Hughes Medical Institute has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Biomedical Informatics Research Network is parent organization of: Cover Pages |
Alzheimer's disease, Dementia, Normal, Nondemented, Aging | NIA P50 AG05681; NIA P01 AG03991; NIA R01 AG021910; NIMH P50 MH071616; NCRR U24 RR021382; NIMH R01 MH56584 |
Free, Acknowledgement required | r3d100012182, nif-0000-00387 | http://www.nitrc.org/projects/oasis https://doi.org/10.17616/R3RS8K |
SCR_007385 | The Open Access Series of Imaging Studies, Open Access Series of Imaging Studies, OASIS | 2026-02-14 02:06:36 | 299 | ||||
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Odor Molecules DataBase Resource Report Resource Website 1+ mentions |
Odor Molecules DataBase (RRID:SCR_007286) | OdorDB | data or information resource, database | OdorDb is a database of odorant molecules, which can be searched in a few different ways. One can see odorant molecules in the OdorDB, and the olfactory receptors in ORDB that they experimentally shown to bind. You can search for odorant molecules based on their attributes or identities: Molecular Formula, Chemical Abstracts Service (CAS) Number and Chemical Class. Functional studies of olfactory receptors involve their interactions with odor molecules. OdorDB contains a list of odors that have been identified as binding to olfactory receptors. | genetics, cellular, molecular, olfactory, receptor, training material |
is related to: Olfactory Receptor DataBase has parent organization: Yale University; Connecticut; USA works with: ORModelDB |
Aging | Human Brain Project ; NIMH ; NIA ; NICD ; NINDS ; Multidisciplinary University Research Initiative ; NIDCD RO1 DC 009977 |
nif-0000-00056 | SCR_007286 | 2026-02-14 02:06:03 | 1 | |||||||
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Olfactory Bulb Odor Map DataBase (OdorMapDB) Resource Report Resource Website |
Olfactory Bulb Odor Map DataBase (OdorMapDB) (RRID:SCR_007287) | OdorMapDB | data or information resource, atlas, database | OdorMapDB is designed to be a database to support the experimental analysis of the molecular and functional organization of the olfactory bulb and its basis for the perception of smell. It is primarily concerned with archiving, searching and analyzing maps of the olfactory bulb generated by different methods. The first aim is to facilitate comparison of activity patterns elicited by odor stimulation in the glomerular layer obtained by different methods in different species. It is further aimed at facilitating comparison of these maps with molecular maps of the projections of olfactory receptor neuron subsets to different glomeruli, especially for gene targeted animals and for antibody staining. The main maps archived here are based on original studies using 2-deoxyglucose and on current studies using high resolution fMRI in mouse and rat. Links are also provided to sites containing maps by other laboratories. OdorMapDB thus serves as a nodal point in a multilaboratory effort to construct consensus maps integrating data from different methodological approaches. OdorMapDB is integrated with two other databases in SenseLab: ORDB, a database of olfactory receptor genes and proteins, and OdorDB, a database of odor molecules that serve as ligands for the olfactory receptor proteins. The combined use of the three integrated databases allows the user to identify odor ligands that activate olfactory receptors that project to specific glomeruli that are involved in generating the odor activity maps. | odor, male, urine, mouse, methyl anisole, patchone, indole, helional, butyrophenone, fenchone, olfactory bulb, fmri, rat, odor ligand, olfactory receptor, smell |
is used by: NIF Data Federation has parent organization: Yale University; Connecticut; USA |
Aging | The Human Brain Project ; NIMH ; NIA ; NICD ; NINDS ; Multidisciplinary University Research Initiative ; NIDCD RO1 DC 009977 |
PMID:15067166 | nif-0000-00057 | SCR_007287 | OdorMap DB, Odor Map Database | 2026-02-14 02:06:36 | 0 |
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