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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ToppCluster Resource Report Resource Website 100+ mentions |
ToppCluster (RRID:SCR_001503) | ToppCluster | production service resource, data analysis service, service resource, resource, analysis service resource | A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene. | term enrichment, gene, analysis, gene enrichment analysis, connectivity, heatmap, ortholog, microarray, function, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenitoUrinary Development Molecular Anatomy Project is related to: ToppGene Suite |
NIDDK 1U01DK70219; NIDDK P30DK078392; NCRR U54 RR025216; NIDCR U01DE020049 |
PMID:20484371 | Free | OMICS_02225, nlx_152801, biotools:toppcluster | https://bio.tools/toppcluster | SCR_001503 | ToppCluster: A multiple gene list feature analyzer for the dissection of biological systems | 2025-04-27 10:28:56 | 137 | ||||
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Gene Weaver Resource Report Resource Website 10+ mentions |
Gene Weaver (RRID:SCR_003009) | production service resource, data repository, data analysis service, service resource, storage service resource, analysis service resource, database, data or information resource | Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration. | phenotype, microarray, gene, genome, functional genomics, process, pathway, function, gene set, genomic data integration, analysis, visualization |
is used by: NIF Data Federation is used by: Integrated Datasets is listed by: OMICtools is related to: Integrated Manually Extracted Annotation has parent organization: Jackson Laboratory |
Integrative Neuroscience Initiative on Alcoholism ; NIAAA U01 AA13499; NIAAA U24 AA13513; NIAAA R01 AA18776 |
PMID:22080549 PMID:19733230 |
Free, Freely available | OMICS_02232, nif-0000-00517 | http://ontologicaldiscovery.org/ | SCR_003009 | GeneWeaver, GeneWeaver - A system for the integration of functional genomics experiments, Ontological Discovery Environment, GeneWeaver.org | 2025-04-27 10:30:21 | 32 | |||||
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TORTOISE Resource Report Resource Website 50+ mentions |
TORTOISE (RRID:SCR_001645) | TORTOISE | data processing software, software resource, image analysis software, software application, image processing software | An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data. | diffusion mri, dti, image motion correction, distortion correction, tensor computation, visualization, analysis, tensor fitting, modeling, magnetic resonance, tensor metric |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: National Institute of Child Health and Human Development |
NICHD | Acknowledgement requested | nlx_153921 | http://www.nitrc.org/projects/tortoise | SCR_001645 | Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble | 2025-04-27 10:29:02 | 90 | |||||
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SEER Datasets and Software Resource Report Resource Website 10+ mentions |
SEER Datasets and Software (RRID:SCR_003293) | software resource, topical portal, data or information resource, disease-related portal, portal | Portal provides SEER research data and software SEER*Stat and SEER*Prep. SEER incidence and population data associated by age, sex, race, year of diagnosis, and geographic areas can be used to examine stage at diagnosis by race/ethnicity, calculate survival by stage at diagnosis, age at diagnosis, and tumor grade or size, determine trends and incidence rates for various cancer sites over time. SEER releases new research data every Spring based on the previous November’s submission of data. | NCI, cancer, statistics, epidemiology, analysis |
lists: SEER*Stat lists: NCI SEER Cancer Stage Variable Documentation is related to: Surveillance Epidemiology and End Results has parent organization: National Cancer Institute |
cancer | NCI | Free, Available through online access/download/DVD | nif-0000-31490 | SCR_003293 | The Surveillance Epidemiology and End Results (SEER) Program, SEER Datasets Software, SEER Datasets & Software, The Surveillance Epidemiology and End Results (SEER) Program of the National Cancer Institute | 2025-04-27 10:30:29 | 23 | ||||||
|
Nitime Resource Report Resource Website 10+ mentions |
Nitime (RRID:SCR_002504) | NiTime | data processing software, software resource, data analysis software, software toolkit, software library, software application | Software library for time-series analysis of data from neuroscience experiments. It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code. | eeg, meg, electrocorticography, magnetic resonance, time-series, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuroimaging in Python |
BSD License | nlx_155903 | http://www.nitrc.org/projects/nitime | SCR_002504 | Nitime: time-series analysis for neuroscience | 2025-04-27 10:29:47 | 19 | ||||||
|
Gene Expression Omnibus (GEO) Resource Report Resource Website 10000+ mentions |
Gene Expression Omnibus (GEO) (RRID:SCR_005012) | GEO | data repository, service resource, storage service resource, database, data or information resource | Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries. | gold standard, genomics, data, repository, microarray, mRNA, DNA, protein, analysis, SAGE, mass spectrometry, dataset |
is used by: ChIPseeker is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Allen Institute for Brain Science has parent organization: NCBI works with: shinyGEO works with: Drug Gene Budger works with: Signaling Pathways Project works with: GEN3VA |
National Library of Medicine | PMID:23193258 PMID:21097893 PMID:18940857 PMID:17160034 PMID:17099226 PMID:16939800 PMID:16888359 PMID:15608262 PMID:11752295 |
Free, Freely available | nif-0000-00142, nlx_96903, OMICS_01030, SCR_007303 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gds http://www.ncbi.nlm.nih.gov/geo/ |
http://www.ncbi.nlm.nih.gov/gds | SCR_005012 | Gene Expression Omnibus (GEO), Entrez GEO DataSets, Gene Expression Data Sets, Gene Expression Omnibus, GEO, NCBI GEO DataSets, GEO DataSets, Gene Expression Omnibus DataSets | 2025-04-27 10:31:37 | 11294 | |||
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Onto-Compare Resource Report Resource Website 1+ mentions |
Onto-Compare (RRID:SCR_005669) | Onto-Compare | production service resource, data analysis service, service resource, analysis service resource, database, data or information resource | Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously. Typically, they have been used in exploratory research to help formulate hypotheses. In most cases, this phase is followed by a more focused, hypothesis driven stage in which certain specific biological processes and pathways are thought to be involved. Since a single biological process can still involve hundreds of genes, microarrays are still the preferred approach as proven by the availability of focused arrays from several manufacturers. Since focused arrays from different manufacturers use different sets of genes, each array will represent any given regulatory pathway to a different extent. We argue that a functional analysis of the arrays available should be the most important criterion used in the array selection. We developed Onto-Compare as a database that can provide this functionality, based on the GO nomenclature. Compare commercially available microarrays based on GO. User account required. Platform: Online tool | microarray, gene, ontology, gene expression, data-mining, browser, visualization, analysis, compare, search engine, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, other analysis, compare commercially available microarrays based on go |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:12664686 PMID:15215428 |
Free for academic use | nlx_149108 | SCR_005669 | 2025-04-27 10:32:00 | 1 | |||||||
|
SPM Resource Report Resource Website 5000+ mentions Issue |
SPM (RRID:SCR_007037) | SPM | data processing software, software resource, data analysis software, image analysis software, software application | Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG. | analysis, brain, imaging, data, sequence, fMRI, PET, SPECT, EEG, MEG, bio.tools |
uses: Neuroimaging Data Model uses: imcalc: SPM batch image calculator is used by: rsfMRI_fconn calculation is used by: Automatic Analysis is used by: auto_acpc_reorient is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite is affiliated with: Clinical Toolbox for SPM is affiliated with: Statistical non-Parametric Mapping is related to: WFU Biological Parametric Mapping Toolbox is related to: vis: SPM Visualized Statistics toolbox is related to: LEAD-DBS is related to: CCHMC Pediatric Brain Templates is related to: IBMA toolbox is related to: ArtRepair for robust fMRI is related to: ASL data processing tool box is related to: BrainVISA / Anatomist is related to: MRIcro Software is related to: xjView: A Viewing Program For SPM is related to: BrainMagix SPM Viewer is related to: MarsBaR region of interest toolbox for SPM is related to: NIRS-SPM is related to: SPM SS - fMRI functional localizers is related to: Wisconsin White Matter Hyperintensities Segmentation Toolbox is related to: Dementia-specific FDG PET Template for SPM analyses is related to: SPM Anatomy Toolbox is related to: MIPAV: Medical Image Processing and Visualization is related to: MATLAB is related to: hMRI-toolbox is related to: Sandwich Estimator Toolbox has parent organization: University College London; London; United Kingdom is required by: MRTool provides: TSDiffAna has plug in: ICN_Atlas works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: NIAG Addiction Data works with: ICN_Atlas works with: spm_auto_reorient_coregister works with: Computational Anatomy Toolbox for SPM works with: FieldTrip works with: POAS4SPM |
Free, Available for download, Freely available | biotools:SPM | https://github.com/spm/spm12 https://bio.tools/SPM |
https://www.fil.ion.ucl.ac.uk/spm/ | SCR_007037 | Statistical Parametric Mapping, SPM5, SPM2, SPM12, Statistical Parametric Mapping Software, SPM99, SPM8, SPM, SPM96 | 2025-04-27 10:33:07 | 8619 | |||||
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Chem Service, Inc. Resource Report Resource Website 1+ mentions |
Chem Service, Inc. (RRID:SCR_008380) | instrument manufacture, production service resource, material service resource, service resource | Chem Service, Inc. offers the convenience, cost savings and reliability of 1,000 Certified Standards Grade Organic Chemicals at your fingertips with our Organic Mini Stockroom Kit. Whether your lab is big or small, disposal fees are a concern. The Organic Mini-stockroom offers you the ability to have 1000 different chemicals at quantities ranging from 100mg to 10gm; thus, reducing disposal costs. Over 95% of their neat Standards Grade materials have a purity of 98.0% or greater, and have been analyzed by three or more (where feasible) independent methods of analysis. These do not require purity corrections when preparing a solution for use with EPA methods. Their more than 13,000 organic and inorganic standards, and solutions, support EPA Methods, ASTM Methods, State UST Methods, Air monitoring Methods, and International Methods. They offer explosive residue standards, PCB congeners, petroleum hydrocarbon standards for the petrochemical industry, pesticide standards, FAME, and vitamin standards for food analysis. Suited for identification of unknowns, product screening, optimal chemical selection and small scale chemical reactions, the O-1000A Organic Ministockroom Kit was designed for laboratories with broad chemical classification and indentification needs. Chem Service, Inc. is registered by ABS Quality Evaluations, Inc., to the internationally recognized requirements of ISO 9001 for design, development, production, distribution and servicing of organic neat and synthetic reference materials. | food, analysis, chemical, industry, method, organic, pestiide, petrochemical, solution, synthetic, vitamin | nif-0000-30016 | SCR_008380 | ChemService | 2025-04-27 10:34:16 | 4 | ||||||||||
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Biocode Commons Resource Report Resource Website |
Biocode Commons (RRID:SCR_024553) | portal, topical portal, data or information resource | Platform provides resources for genomic observations from collection to analysis and publication. Works with standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets. Biocode Commons is also collaborating on development of Biological Collections Ontology, working to better integrate ontologies, vocabularies, and relevant standards that are related to BCO. | Biological Collections Ontology, Biological Collections Ontology development, genomic observations, collection, analysis, publication, standards community, |
is listed by: DataCite is listed by: University of California; California; USA has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.7286 | SCR_024553 | 2025-04-27 10:44:20 | 0 | |||||||||
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Bern-Barcelona EEG database Resource Report Resource Website 1+ mentions |
Bern-Barcelona EEG database (RRID:SCR_001582) | Bern-Barcelona EEG database | source code, data set, software resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented November 23, 2020; EEG data set, source code, and results from 7500 signal pairs from 5 epilepsy patients analyzed in the manuscript, Andrzejak RG, Schindler K, Rummel C. Nonrandomness, nonlinear dependence, and nonstationarity of electroencephalographic recordings from epilepsy patients. Phys. Rev. E, 86, 046206, 2012. All Matlab source codes are included in the file ASR_Sources_2012_10_16.zip. The clinical purpose of these recordings was to delineate the brain areas to be surgically removed in each individual patient in order to achieve seizure control. | eeg, electroencephalogram, epilepsy, intracranial, eeg recording, signal, analysis, time series, nonlinear, surrogate signal, surrogate, matlab, focal, non-focal, signal | has parent organization: Pompeu Fabra University; Barcelona; Spain | Epilepsy, Pharmacoresistant focal-onset epilepsy, Seizure | Spanish Ministry of Education and Science grant FIS-2010-18204; Swiss National Science Foundation SNF 320030-122010; Swiss National Science Foundation SNF 33CM30-124089 |
PMID:23214662 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153819 | http://ntsa.upf.edu/downloads/andrzejak-rg-schindler-k-rummel-c-2012-nonrandomness-nonlinear-dependence-and, http://www.dtic.upf.edu/~ralph/sc/ | SCR_001582 | 2025-04-27 10:28:59 | 3 | ||||
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DPARSF Resource Report Resource Website 500+ mentions |
DPARSF (RRID:SCR_002372) | DPARSF | data processing software, software toolkit, software application, software resource | A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely. | magnetic resonance, fmri, resting-state fmri, matlab, analysis, brain |
is used by: DPABI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China has parent organization: RFMRI.ORG |
PMID:20577591 | GNU General Public License | nlx_155735 | http://www.nitrc.org/projects/dparsf | SCR_002372 | Data Processing Assistant for Resting-State fMRI | 2025-04-27 10:29:38 | 512 | |||||
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Fusion ICA Toolbox Resource Report Resource Website 10+ mentions |
Fusion ICA Toolbox (RRID:SCR_003494) | FIT | data processing software, software toolkit, software application, software resource | A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1 | analysis, functional magnetic resonance imaging, cca, image, eeg, neuroimaging, matlab, smri, snp, mri, algorithm, reusable library, independent component analysis, principal component analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of New Mexico; New Mexico; USA |
NIBIB 1RO1EB005846; NSF 0612076 |
GNU General Public License | nif-0000-36743 | http://www.nitrc.org/projects/fit | SCR_003494 | Fusion ICA Toolbox (FIT) | 2025-04-27 10:30:35 | 13 | |||||
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Gephi Resource Report Resource Website 1000+ mentions |
Gephi (RRID:SCR_004293) | Gephi | data processing software, software application, software resource | Open-source software for network visualization and analysis helping data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. It uses a 3D render engine to display large graphs in real-time and to speed up the exploration. Gephi combines built-in functionalities and flexible architecture to: explore, analyze, spatialize, filter, cluterize, manipulate and export all types of networks. Gephi runs on Windows, Linux and Mac OS X. Gephi is based on a visualize-and-manipulate paradigm which allow any user to discover networks and data properties. Moreover, it is designed to follow the chain of a case study, from data file to nice printable maps. It is open-source and free (GNU General Public License). Applications: * Exploratory Data Analysis: intuition-oriented analysis by networks manipulations in real time. * Link Analysis: revealing the underlying structures of associations between objects, in particular in scale-free networks. * Social Network Analysis: easy creation of social data connectors to map community organizations and small-world networks. * Biological Network analysis: representing patterns of biological data. * Poster creation: scientific work promotion with hi-quality printable maps. Gephi 0.7 architecture is modular and therefore allows developers to add and extend functionalities with ease. New features like Metrics, Layout, Filters, Data sources and more can be easily packaged in plugins and shared. The built-in Plugins Center automatically gets the list of plugins available from the Gephi Plugin portal and takes care of all software updates. Download, comment, and rate plugins provided by community members and third-party companies, or post your own contributions! | network, visualization, visual analytics, exploratory data analysis, graph, analysis, open source, plugin, filter, cluter, manipulate, export | is parent organization of: Diseasome | GNU General Public License | nlx_31183 | SCR_004293 | 2025-04-27 10:31:02 | 2496 | ||||||||
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FIVA - Functional Information Viewer and Analyzer Resource Report Resource Website 1+ mentions |
FIVA - Functional Information Viewer and Analyzer (RRID:SCR_005776) | FIVA | data processing software, software application, software resource | Functional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, gene expression, gene expression pattern, functional profile, statistical analysis, metabolic pathway, gene ontology, function, ortholog, gene regulatory interaction, biological process, transcriptome, visualization, analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: MolGen |
Netherlands Organization for Scientific Research ; industrial partners in the NWO-BMI project number 050.50.206 on Computational Genomics of Prokaryotes ; Center IOP Genomics ; European Union QLK3-CT-2001-01473 |
PMID:17237043 | Free for academic use | nlx_149245 | SCR_005776 | FIVA - Functional Information Viewer Analyzer, Functional Information Viewer and Analyzer (FIVA), Functional Information Viewer and Analyzer | 2025-04-27 10:32:03 | 1 | |||||
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GoBean - a Java application for Gene Ontology enrichment analysis Resource Report Resource Website 10+ mentions |
GoBean - a Java application for Gene Ontology enrichment analysis (RRID:SCR_005808) | GoBean | data processing software, software application, software resource | GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible | java, gene ontology, ontology, gene association, analysis, enrichment, term enrichment |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Gachon University of Medicine and Science; Incheon; South Korea |
PMID:22360891 | Free for academic use | nlx_149296 | http://neon.gachon.ac.kr/GoBean/ | SCR_005808 | 2025-04-27 10:32:04 | 22 | ||||||
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SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_007075) | data processing software, software application, software resource | A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options. | gene, gene expression, function, analysis, visualization, statistical analysis, windows, c#, gene function, chromosome location, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Gene Expression Omnibus |
PMID:14988116 | Free | nlx_149285, biotools:seqexpress | https://bio.tools/seqexpress | SCR_007075 | 2025-04-27 10:33:10 | 0 | |||||||
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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 |
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 | 2025-04-27 10:32:48 | 15 | |||||
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Homer2 Resource Report Resource Website 100+ mentions |
Homer2 (RRID:SCR_009586) | image analysis software, data processing software, software application, software resource | Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data. | Analysis, optical, imaging, fnirs, map, brain, activation, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NIRx2nirs: A NIRx to .nirs data converter |
NIBIB EB025145; NIBIB R01 EB006385; NCRR P41 RR14075 |
Free, Available for download, Freely available | nlx_155773 | http://www.nitrc.org/projects/homer2 https://homer-fnirs.org/ |
SCR_009586 | HOMER1, Photon Migration Imaging toolbox | 2025-04-27 10:35:14 | 178 | ||||||
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DSI Studio Resource Report Resource Website 100+ mentions |
DSI Studio (RRID:SCR_009557) | DSI Studio | image analysis software, data processing software, software application, software resource | A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system. | analyze, c++, console (text based), dicom, diffusion mr fiber tracking, diffusion spectrum, fiber tracking, image reconstruction, linux, microsoft, modeling, magnetic resonance, nifti, posix/unix-like, q-ball, quantification, super tensor, tensor metric, tractography, visualization, win32 (ms windows), windows, coregistration, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Carnegie Mellon University; Pennsylvania; USA |
BSD License | nlx_155737 | http://www.nitrc.org/projects/dsistudio | SCR_009557 | 2025-04-27 10:35:13 | 488 |
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