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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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RAVE Resource Report Resource Website 1+ mentions |
RAVE (RRID:SCR_019040) | software resource, software application, data analysis software, data processing software, data visualization software | 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 | 2026-02-12 09:47:08 | 1 | ||||||||
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SnapATAC Resource Report Resource Website 10+ mentions |
SnapATAC (RRID:SCR_020981) | software toolkit, software resource, software application, data analysis software, data processing software | 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 | 2026-02-12 09:47:13 | 22 | |||||||
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Track-A-Worm Resource Report Resource Website 1+ mentions |
Track-A-Worm (RRID:SCR_018299) | software resource, software application, data analysis software, data processing software | 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 | 2026-02-12 09:47:01 | 3 | |||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | analysis service resource, software resource, data access protocol, service resource, web service, production service 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 | 2026-02-12 09:46:54 | 4 | ||||||||
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EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | software toolkit, software resource, software application, data analysis software, data processing software | 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 | 2026-02-12 09:46:53 | 7 | ||||||
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Scalable Analytics for Brain Exploration Research Resource Report Resource Website 1+ mentions |
Scalable Analytics for Brain Exploration Research (RRID:SCR_018812) | SABER, saber | software toolkit, workflow software, software resource, software application, data processing software, software library | 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 | 2026-02-12 09:46:56 | 1 | |||||||
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PIVOT software Resource Report Resource Website 10+ mentions |
PIVOT software (RRID:SCR_017210) | PIVOT | software resource, software application, data analysis software, data processing software | 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 | 2026-02-12 09:46:50 | 17 | ||||||
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Brain Image Library Resource Report Resource Website 10+ mentions |
Brain Image Library (RRID:SCR_017272) | BIL | data or information resource, storage service resource, service resource, data repository | 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 | 2026-02-12 09:46:47 | 16 | ||||
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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, service resource, storage service resource, database, 3d spatial image, data or information resource, image | 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 | 2026-02-12 09:47:05 | 27 | |||||
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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 | 2026-02-12 09:46:53 | 2 | ||||||||
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gene Expression Analysis Resource Resource Report Resource Website 50+ mentions |
gene Expression Analysis Resource (RRID:SCR_017467) | gEAR | analysis service resource, software resource, service resource, production service resource, data or information resource, portal | 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 | 2026-02-12 09:47:09 | 76 | |||||||
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TReNA Resource Report Resource Website |
TReNA (RRID:SCR_017458) | software resource, network analysis software, software application, data analysis software, data processing software | 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 | 2026-02-12 09:46:53 | 0 | |||||||||
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ChromHMM Resource Report Resource Website 10+ mentions |
ChromHMM (RRID:SCR_018141) | software resource, software application, data analysis software, data processing software | 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 | 2026-02-12 09:47:00 | 47 | ||||||
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Autism Genetic Resource Exchange Resource Report Resource Website 1+ mentions |
Autism Genetic Resource Exchange (RRID:SCR_004403) | AGRE | material resource, biomaterial supply resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A private repository of clinical and genetic information on families with autism. Genetic and clinical data are obtained from families that have more than one family member diagnosed with an Autism Spectrum Disorder. The biological samples, along with the accompanying clinical data, are made available to AGRE-approved researchers worldwide. As they become available, additional family pedigrees will be posted in the online catalog. Cell lines have been established for the majority of families in this collection and serum/plasma is available on a subset of the subjects until stocks are depleted. The diagnosis of autism has been made using the standard Autism Diagnostic Interview-Revised (ADI-R) algorithm and the Autism Diagnostic Observation Scale (ADOS-G). Detailed birth and medical histories (including basic dysmorphology assessments) on children as well as family and medical information for parents and unaffected siblings, are available for nearly all families. DNA, cell lines, serum, plasma and clinical information are made available to AGRE-approved researchers for analysis. | family registry, gene bank, genetics, autism diagnostic, interview, autism diagnostic observational scale, autism spectrum disorder, birth, clinical data, genome scan, genotypic data, medical history, pedigree, phenotypic data, dna, cell line, serum, plasma, biorepository, biospecimen, pervasive development disorder |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Autism Speaks |
Autism, Autism spectrum disorder, Pervasive Development Disorder | NIMH 1U24MH081810 | PMID:20955925 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00226 | SCR_004403 | 2026-02-12 09:43:50 | 1 | |||||
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TADA-A Resource Report Resource Website |
TADA-A (RRID:SCR_024538) | source code, software resource | Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies. | mapping risk genes, de novo mutations, whole genome sequencing, | NIMH R01MH110531; Simons Foundation |
PMID:29754769 | Free, Available for download, Freely available | SCR_024538 | TADA-Annotations | 2026-02-12 09:48:17 | 0 | ||||||||
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Early Postnatal Developmental Mouse Brain Atlas Resource Report Resource Website 1+ mentions |
Early Postnatal Developmental Mouse Brain Atlas (RRID:SCR_024725) | epDevAtlas | organization portal, atlas, data or information resource, portal, laboratory portal | Suite of open access resources including 3D atlases of early postnatally developing mouse brain and mapped cell type density growth charts, which can be used as standalone resources or to implement data integration. Web platform can be utilized to analyze and visualize the spatiotemporal growth of GABAergic, microglial, and cortical layer-specific cell type densities in 3D. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system with an isotropic resolution of 20 μm (XYZ in coronal plane). Average transformations were conducted at 20 μm voxel resolution by interpolating high resolution serial two photon tomography images from primarily Vip-IRES-Cre;Ai14 mice at postnatal (P) ages P4, P6, P8, P10, P12, and P14. For all ages, anatomical labels from the P56 Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) were iteratively down registered to each early postnatal time point in a non-linear manner, aided by manual parcellations of landmarks in 3D, consistent with the Allen Mouse Reference Atlas Ontology. | 3D atlases, early postnatally developing mouse brain, mapped cell type density growth charts, Allen Mouse Reference Atlas Ontology, |
uses: Allen Mouse Reference Atlas Ontology uses: Allen Mouse Brain Common Coordinate Framework is organization facet of: BRAIN Initiative Cell Atlas Network |
NIMH RF1MH12460501; NINDS R01NS108407 |
DOI:10.1101/2023.11.24.568585 | Free, Freely available | SCR_024725 | 2026-02-12 09:48:16 | 3 | |||||||
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XTRACT Resource Report Resource Website 1+ mentions |
XTRACT (RRID:SCR_024933) | software application, software resource | Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain. | automated tractography, tractography, human, macaque, brain | is a plug in for: FSL | Medical Research Council PhD Studentship UK ; Marie Skłodowska-Curie Individual Fellowship Grant ; Biotechnology and Biological Sciences Research Council ; Netherlands Organization for Scientific Research NWO Netherlands ; Sir Henry Dale Wellcome Trust Fellowship UK ; MRC Career Development Fellowship UK ; Wellcome Trust Collaborative Award UK ; UK Engineering and Physical Sciences Research Council ; Wellcome Trust grant UK ; Human Connectome Project ; NIMH 1U54MH091657; McDonnell Center for Systems Neuroscience at Washington University ; NIH ; UK Biobank Resource ; Wellcome Trust |
PMID:32407993 | Free, Freely available | SCR_024933 | 2026-02-12 09:48:08 | 2 | ||||||||
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eddyqc Resource Report Resource Website |
eddyqc (RRID:SCR_024936) | software resource, software application, data analysis software, data processing software | Software tool allows to assess dMRI data both at single subject and group levels.Calculates average SNR across all voxels within brain mask to give summary measure of overall quality of dataset. Used to generate single subject and study wise reports and databases. | assess dMRI data, voxels within brain mask, summary measure of overall data quality, generate single subject and study wise reports, | is a plug in for: FSL | European Research Council ; UK Medical Research Council ; Wellcome-Trust Strategic Award ; NIMH 1U01MH109589; NIMH 1U01AG052564; NIMH 1U54MH091657 |
PMID:30267859 | Free, Freely available | https://git.fmrib.ox.ac.uk/matteob/eddy_qc_release | SCR_024936 | 2026-02-12 09:48:21 | 0 | |||||||
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Guided Sparse Factor Analysis Resource Report Resource Website 1+ mentions |
Guided Sparse Factor Analysis (RRID:SCR_025023) | GSFA | software toolkit, software resource | Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data. | sparse factor analysis, differential gene expression, discovery simultaneously, single cell CRISPR screening data, | NIMH R01MH110531; NHGRI R01HG010773; NIMH R01MH116281; NIGMS R01 GM126553; NHGRI R01 HG011883; NSF ; Sloan Research Fellowship |
PMID:37770710 | Free, Available for download, Freely available | SCR_025023 | 2026-02-12 09:48:19 | 1 | ||||||||
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MatrixEQTL Resource Report Resource Website 50+ mentions |
MatrixEQTL (RRID:SCR_025513) | software resource, software application, data analysis software, data processing software | Software tool for ultra fast eQTL analysis via large matrix operations. | expression Quantitative Trait Loci, fast eQTL analysis, large matrix operations, | NIMH R01 MH090936; NIEHS R01 ES015241; US Environmental Protection Agency ; NCI R01 CA138255; NSF ; Gillings Innovation Laboratory in Statistical Genomics |
PMID:22492648 | Free, Freely available, | SCR_025513 | Matrix Expression Quantitative Trait Loci | 2026-02-12 09:49:01 | 69 |
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