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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-02-13 10:57:56 | 76 | |||||||
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Analysis, Visualization, and Informatics Lab-space (AnVIL) Resource Report Resource Website 10+ mentions |
Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) | AnVIL | data repository, storage service resource, portal, data or information resource, service resource, project portal | Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces. | Dataset, NHGRI, program, NIH, initiative, funded, human, genomic, data, access, sharing, FAIR, analysis, workflow |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
NIH | Restricted | https://www.genome.gov/Funded-Programs-Projects/Computational-Genomics-and-Data-Science-Program/Genomic-Analysis-Visualization-Informatics-Lab-space-AnVIL | SCR_017469 | Visualization, and Informatics Lab-space, AnVIL, Analysis Visualization and Informatics Lab-space, Analysis | 2026-02-13 10:58:04 | 24 | ||||||
|
Hemodialysis Pilot Studies Consortium Resource Report Resource Website |
Hemodialysis Pilot Studies Consortium (RRID:SCR_017468) | HDPSC | data or information resource, organization portal, portal, consortium | Consortium to design and conduct pilot and feasibility studies of novel therapies to reduce morbidity and mortality for patients treated with maintenance hemodialysis. Data Coordinating Center (DCC) for consortium provides scientific expertise and operational support for pilot studies that will be conducted at HDPSC Participating Clinical Centers. Data Coordinating Center for Hemodialysis Pilot Studies Consortium. | Novel, therapy, reduce, morbidity, patient, maintenance, hemodialysis, data, coordinating, center | has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA | NIH ; NIDDK |
SCR_017468 | 2026-02-13 10:57:58 | 0 | |||||||||
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Connectome Computation System Resource Report Resource Website 10+ mentions |
Connectome Computation System (RRID:SCR_017342) | CCS | data analysis software, software resource, data processing software, software application | Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies. | Multimodal, human, brain, imaging, data, analysis, connectome, magnetic, resonance | DOI:10.1007/s11434-014-0698-3 | Free, Available for download, Freely available | SCR_017342 | 2026-02-13 10:58:01 | 15 | |||||||||
|
miRpathDB Resource Report Resource Website 50+ mentions |
miRpathDB (RRID:SCR_017356) | web service, data or information resource, data access protocol, software resource, database | Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are. | Collection, miRNA, data, pathway, gene, ontology, dataset, dictionary, target, regulation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Saarland University ; Germany |
PMID:27742822 | biotools:miRPathDb | https://bio.tools/miRPathDB | SCR_017356 | miRNA Pathway Dictionary Database | 2026-02-13 10:57:56 | 52 | ||||||
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fastMNN Resource Report Resource Website 1+ mentions |
fastMNN (RRID:SCR_017351) | data analysis software, software resource, data processing software, software application | Software tool to correct for batch effects in single-cell expression data using fast version of mutual nearest neighbors (MNN) method. | Correct, batch, effect, single, cell, expression, data, fast, version, mutual, nearest, neighbors | Free, Available for download, Freely available | SCR_017351 | Fast Mutual Nearest Neighbors | 2026-02-13 10:57:56 | 7 | ||||||||||
|
Mediation Analysis of Causality under Confounding Resource Report Resource Website |
Mediation Analysis of Causality under Confounding (RRID:SCR_017442) | MACC | data analysis software, software resource, data processing software, software application | Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method. | Casual, mediation, analysis, confounding, correlated, error, data, hierarchical, structure, parameter, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: CRAN |
NIBIB EB022911 | Free, Available for downloads, Freely available | SCR_017442 | Mediation Analysis of Causality under Confounding, macc | 2026-02-13 10:58:03 | 0 | |||||||
|
Transcriptomics Explorer Resource Report Resource Website 50+ mentions |
Transcriptomics Explorer (RRID:SCR_017567) | data visualization software, data processing software, data analysis software, service resource, software application, software resource | Software tool to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in web browser. To explore gene expression heatmap across cell types in datasets, search for genes of interest, explore tSNE visualization, colored by cell types or expression of genes of interest, visualize dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions, find cell type of interest in one visualization and see its characteristics in different visualization.Used for Allen Brain Map Cell Types Database to Browse Data: Human - Multiple Cortical Areas, and Mouse - Cortex and Hippocampus. | Visualize, analyze, transcriptomic, data, cell, type, mouse, human, Allen, database, multiple, cortical, area, cortex, hippocampus | works with: Allen Brain Atlas | Free, Freely available | https://celltypes.brain-map.org/rnaseq/human/cortex https://celltypes.brain-map.org/rnaseq/mouse/cortex-and-hippocampus |
SCR_017567 | 2026-02-13 10:57:59 | 78 | |||||||||
|
Willoughby–Hoye Python Scripts A-D Resource Report Resource Website 1+ mentions Issue |
Willoughby–Hoye Python Scripts A-D (RRID:SCR_017562) | data analysis software, software resource, data processing software, software application | Software tool as scripts for calculating NMR chemical shifts. Warning - this group of Python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain bug. Please see PMID:31591889. | Python, NMR, script, caluclating, chemical, shift, data | NIA R01 AG039468 | PMID:24556787 PMID:31591889 |
Free, Freely available | SCR_017562 | 2026-02-13 10:57:59 | 1 | |||||||||
|
SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | ontology, data analysis service, analysis service resource, data or information resource, production service resource, service resource, controlled vocabulary | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard ; European Union ; CERCA Program/Generalitat de Catalunya ; NINDS NS36251; German Federal Ministry of Education and Research |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-02-13 10:58:01 | 134 | |||||||
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Project DARE Resource Report Resource Website |
Project DARE (RRID:SCR_017538) | DARE | portal, consortium, data or information resource, organization portal, project portal | EU data infrastructure with workflow connectivity layer. Common Workflow Language. Project pioneers methodologies and integrated set of supporting technologies that will transform European RIs productivity and rate of innovation when three challenges – extreme data, extreme computation and extreme complexity – are faced simultaneously. | European Union, infrastructure, workflow, connectivity, layer, methodology, integrated, data, Agile | European Union | SCR_017538 | project-dare, Delivering Agile Research Excellence on European e-Infrastructures | 2026-02-13 10:57:57 | 0 | |||||||||
|
STRENDA Resource Report Resource Website 1+ mentions |
STRENDA (RRID:SCR_017422) | STRENDA | data repository, storage service resource, data or information resource, service resource, database | Storage and search platform supported by Beilstein-Institut that incorporates STRENDA Guidelines. For authors who prepare manuscript containing functional enzymology data, STRENDA DB provides means to ensure that data sets are complete and valid before submitting them to journal. | Storage, Beilstein Institut, functional, enzymology, data, complition, validation, dataset, guideline, standard, reporting |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: re3data.org is listed by: FigShare |
Restricted | DOI:10.22011, DOI:10.17616/R3536N, DOI:10.25504/FAIRsharing.ekj9zx, r3d100012329 | http://www.strenda-db.org/ https://doi.org/10.17616/R3536N https://doi.org/10.17616/r3536n https://doi.org/10.22011/ https://dx.doi.org/10.22011/ https://fairsharing.org/10.25504/FAIRsharing.ekj9zx https://doi.org/10.17616/R3536N |
SCR_017422 | , Standards for Reporting Enzymology Data, Beilstein-Institut, STRENDA | 2026-02-13 10:57:57 | 3 | ||||||
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SICAS Medical Image Repository Resource Report Resource Website 1+ mentions |
SICAS Medical Image Repository (RRID:SCR_017420) | data repository, storage service resource, service resource | Medical image repository to store medical research data. | Medical, image, repository, store, data |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Free, Freely available | r3d100011560 | https://doi.org/10.17616/R3HP8C | SCR_017420 | Medical Image Repository, SICAS, SICAS Medical Image Repository | 2026-02-13 10:57:59 | 5 | |||||||
|
TempEst Resource Report Resource Website 100+ mentions |
TempEst (RRID:SCR_017304) | data processing software, data analysis software, software toolkit, software application, software resource | Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019. | temporal, signal, clocklikeness, molecular, phylogeny, visualization, analysis, temporally, sampled, sequenced, data, identify, genetic, incongruent | is related to: BEAST | EU Seventh Framework Programme ; ERC Grant |
DOI:doi.org/10.1093/ve/vew007 | Restricted | http://tree.bio.ed.ac.uk/software/tempest/ | SCR_017304 | Path-O-Gen, tempest | 2026-02-13 10:57:58 | 152 | ||||||
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European Variation Archive (EVA) Resource Report Resource Website 50+ mentions |
European Variation Archive (EVA) (RRID:SCR_017425) | EVA | data repository, storage service resource, data or information resource, service resource, database | Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser. | Collection, genetic, variation, data, chromosomal, location, dbSNP, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:eva | https://bio.tools/eva | SCR_017425 | EVA, European Variation Archive | 2026-02-13 10:57:56 | 89 | ||||||
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Single Cell Developmental Database Resource Report Resource Website 1+ mentions |
Single Cell Developmental Database (RRID:SCR_017546) | SCDevDB | data repository, storage service resource, data set, data or information resource, service resource, database | Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes. | Single, cell, gene, expression, profile, human, development, process, data | RGC General Research Fund ; GRF Research Project |
DOI:10.3389/fgene.2019.00903 | Free, Available for download, Freely available | SCR_017546 | Single-Cell Developmental Database | 2026-02-13 10:57:57 | 2 | |||||||
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Transcriptive Resource Report Resource Website |
Transcriptive (RRID:SCR_017545) | data processing software, data analysis software, software toolkit, software application, software resource | Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results. | Analysis, pipeline, RNA, sequencing, data, raw, FastQ, input, align, read, gene, transcript, count, quality, control | Free, Available for download, Freely available | SCR_017545 | 2026-02-13 10:58:01 | 0 | |||||||||||
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Morpheus by Broad Institute Resource Report Resource Website 1000+ mentions |
Morpheus by Broad Institute (RRID:SCR_017386) | data visualization software, data processing software, data analysis software, service resource, software application, software resource | Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis. | Matrix, visualization, analysis, heatmap, input, data, Java | has parent organization: Broad Institute | Free, Available for download, Freely available | https://github.com/cmap/morpheus.js | SCR_017386 | 2026-02-13 10:57:57 | 1704 | |||||||||
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CLC Genomics Server Resource Report Resource Website 10+ mentions |
CLC Genomics Server (RRID:SCR_017396) | data analysis software, software resource, data processing software, software application | Commercially available software tool for high throughput sequencing analysis, designed for use on central compute cluster or server. Can handle data volumes beyond capacity of desktop systems and manages submission of many jobs via its own queuing system or through submission of jobs to third party grid scheduler. | high, throughput, sequencing, analysis, data | works with: CLC Genomics Workbench | Restricted | SCR_017396 | 2026-02-13 10:57:59 | 18 | ||||||||||
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ScanImage Resource Report Resource Website 500+ mentions |
ScanImage (RRID:SCR_014307) | data processing software, data acquisition software, software application, software resource, signal processing software | Open source software application for laser scanning microscopy, electrophysiology, laser scanning photostimulation, and other physiological methods focused on neurobiology. Used to control laser scanning microscopes without need for custom data acquisition hardware. Standard data acquisition boards are used to acquire data and control laser scanning. The tasks of signal integration and image processing are placed on the computer CPU. Multiple versions of ScanImage are available, each with their own features. | Laser, scanning, microscopy, electrophysiology, photostimulation, neurobiology, control, data, acquisition, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: Cold Spring Harbor Laboratory has parent organization: Northwestern University; Illinois; USA |
PMID:12801419 | Restricted | http://scanimage.vidriotechnologies.com/display/SIH/ScanImage+Home | SCR_014307 | Scan Image, ScanImage | 2026-02-13 10:57:17 | 810 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
