Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
histoCAT Resource Report Resource Website 1+ mentions |
histoCAT (RRID:SCR_026499) | software resource, software toolkit, source code | Software package to visualize and analyse multiplexed image cytometry data interactively. | visualize and analyse multiplexed image, image cytometry data, interactively | NIA R01AG066027; NIMH U19MH114830 |
PMID:28783155 | Free, Available for download, Freely available | SCR_026499 | Histology Topography Cytometry Analysis Toolbox | 2026-09-05 06:35:23 | 4 | ||||||||
|
Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | software resource, software toolkit, source code | Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences. | Borzoi models access, convolutional neural networks, predict RNA-seq coverage, | Common Fund of the Office of the Director ; NCI ; NHGRI ; NHLBI ; NIDA ; NIMH ; NINDS |
PMID:39779956 | Free, Available for download, Freely available | SCR_026619 | 2026-09-05 06:35:27 | 2 | |||||||||
|
Ecosystem for Multi-modal Brain-behavior Experimentation and Research Resource Report Resource Website 1+ mentions |
Ecosystem for Multi-modal Brain-behavior Experimentation and Research (RRID:SCR_026700) | EMBER | data or information resource, data repository, service resource, storage service resource | BRAIN Initiative data archive for multi-modal neurophysiological and behavioral data, supporting the Brain Behavior Quantification and Synchronization (BBQS) Program. Accessible and versatile data archive for storage, processing, and curation of multimodal neurophysiological and behavioral datasets. EMBER extends established BRAIN Initiative data infrastructure, provides new data harmonization and synchronization capabilities, and supports scalable integrations for data coordination and AI driven batch processing to enable the goals of the BBQS program. | data archive, multi-modal neurophysiological data, behavioral data, Brain Behavior Quantification and Synchronization (BBQS) Program, |
is related to: Distributed Archives for Neurophysiology Data Integration is related to: Brain Observatory Storage Service and Database (BossDB) has parent organization: BRAIN Initiative has parent organization: Johns Hopkins University; Maryland; USA |
NIDA R24DA064430; NIMH R24MH136632 |
Free, Freely available | SCR_026700 | , Ecosystem for Multi-modal Brain-behavior Experimentation and Research (EMBER), EMBER Archive | 2026-09-05 06:35:29 | 8 | |||||||
|
SIMS Resource Report Resource Website 1+ mentions |
SIMS (RRID:SCR_025787) | software application, software resource | Software label transfer tool for single-cell RNA sequencing analysis. Scalable, Interpretable Modeling for Single-cell RNA-seq data classification. | label transfer, single-cell RNA sequencing analysis, single-cell RNA-seq data classification, | NHGRI 1RM1HG011543; NIMH 1U24MH132628; NSF ; QualcommInstitute ; Schmidt Futures ; University of California Office of the President |
PMID:38823397 | Free, Available for download, Freely available | SCR_025787 | scalable, interpretable machine learning for single cell | 2026-09-05 06:35:07 | 2 | ||||||||
|
CellTax vignette Resource Report Resource Website 1+ mentions |
CellTax vignette (RRID:SCR_017000) | data or information resource, data set | Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing. | data, classification, cell, type, mammalian, brain, cellular, taxonomy, mouse, visual, cortex, gene, expression, pattern, cortical, region |
is related to: Allen Brain Atlas API is related to: Allen Mouse Brain Reference Atlas is related to: Allen Cell Types Database has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Allen Institute for Brain Science ; NEI R01 EY023173; NIMH U01 MH105982 |
PMID:26727548 | Free, Public | SCR_017000 | Cellular Taxonomy of the Mouse Visual Cortex, Cellular Taxonomy of the Mouse Visual Cortex Allen Institue for Brain Science | 2026-09-05 06:34:10 | 3 | |||||||
|
PIANO:Probabilistic Inference Autoencoder Networks for multi-Omics Resource Report Resource Website 1+ mentions |
PIANO:Probabilistic Inference Autoencoder Networks for multi-Omics (RRID:SCR_027864) | PIANO | software application, software resource, source code | Software novel variational autoencoder framework for inferring integrated latent space representations for single cell transcriptomics data that uses a negative binomial generalized linear model for stronger batch correction, and code compilation for ten times faster training than existing tools. Enables superior analyses of multiple atlases, solving challenging integration tasks across sequencing platforms, development, and species, while simultaneously preserving desired biological signals. | Probabilistic Inference Autoencoder Networks, multi-Omics, variational autoencoder framework, inferring integrated latent space representations, single cell transcriptomics data, | is organization facet of: BRAIN Initiative Cell Atlas Network | NIMH 5T32MH065214; NIMH DP2MH140136; NIMH UM1MH130981 |
DOI:10.1101/2025.11.16.686778v2.full#sec-17 | Free, Available for download, Freely available | https://github.com/NingWang1729/piano | SCR_027864 | piano | 2026-09-05 06:36:00 | 2 | |||||
|
CrossExpression Resource Report Resource Website 1+ mentions |
CrossExpression (RRID:SCR_027990) | software resource, software toolkit | Software package to discover genes that coordinate their expression across spatially adjacent cells. Used for analysis of spatial transcriptomic data allowing in-depth analyses how genes coordinate their expression in space to perform tissue-level functions. Facilitates analysis and exploration of cross-expression patterns. | analysis of spatial transcriptomic data, genes, coordinate genes expression in space, cross-expression patterns, | is organization facet of: BRAIN Initiative Cell Atlas Network | NIMH DP2MH132940; NIMH R01MH113005; NIMH R01MH133181; Ontario Graduate Scholarship ; University of Toronto |
PMID:41163012 | Free, Available for download, Freely available | SCR_027990 | 2026-09-05 06:36:04 | 2 | ||||||||
|
NIMP Analytics Resource Report Resource Website 1+ mentions |
NIMP Analytics (RRID:SCR_028218) | NIMP | data access protocol, data or information resource, portal, project portal, software resource, web service | Neuroanatomy-anchored Information Management Platform for collaborative BICAN data generation developed by UTHealth Houston. Serves as metadata tracking engine to support generation, management, and sharing of brain research data. Integrates data production pipelines across brain banks, laboratories, sequencing centers, and data archives. Platform enables integrative and collaborative, consortium-scale FAIR data generation within the BICAN project. Platform is designed to manage complex dataset, including tissue samples and sequencing data, through Specimen Portal and Sequence Library Portal. Portals provide multiple types of data interfaces through dashboards, APIs, faceted queries, and batch data ingestion and exporting. | FAIR, BICAN, CUBIE, Sample Tracking, Data Ecosystem, Brain Tissue, Multi-Omics Profiling Expression Database, neuroanatomy, collaborative BICAN data generation, | is organization facet of: BRAIN Initiative Cell Atlas Network | NIMH U24MH130988 | PMID:41573954 | Free, Freely available, | https://brain-specimenportal.org | SCR_028218 | Neuroanatomy-Anchored Information Management Platform (NIMP) | 2026-09-05 06:36:08 | 1 | |||||
|
dreamlet Resource Report Resource Website 1+ mentions |
dreamlet (RRID:SCR_028168) | software resource, software toolkit, source code | Software R package enables differential expression analysis on multi-sample single cell datasets using linear (mixed) models with precision weights. | Perform differential expression analysis, multi-sample single cell datasets, linear mixed models, precision weights, | NIA P30AG066514; NIA R01AG050986; NIA R01AG065582; NIA R01AG067025; NIMH R01MH109677; NIMH R01MH125246; NIMH RF1MH128970; NIMH U01MH116442; NINDS U01NS125580 |
PMID:36993704 | Free, Available for download, Freely available | SCR_028168 | 2026-09-05 06:36:07 | 1 | |||||||||
|
Factorial Mass Univariate Toolbox Resource Report Resource Website |
Factorial Mass Univariate Toolbox (RRID:SCR_028612) | software resource, software toolkit | Software toolbox (FMUT) is an extension to David Groppe’s Mass Univariate ERP Toolbox (MUT). MUT implements t-tests for several different mass univariate approaches to the analysis of ERP data. FMUT adds to this by implementing one-way and factorial ANOVA versions of the same mass univariate approaches. | NICHD R01 HD082527; NIMH R01 MH071635 |
PMID:31456213 | Free, Available for download, Freely available | https://github.com/ericcfields/FMUT | SCR_028612 | , Factorial Mass Univariate ERP Toolbox, Factorial Mass Univariate ERP Toolbox (FMUT) | 2026-09-05 06:36:16 | 0 | ||||||||
|
PERI: Prospective Evaluation of Reproductive aging Indicators Resource Report Resource Website |
PERI: Prospective Evaluation of Reproductive aging Indicators (RRID:SCR_028698) | software resource, software toolkit, source code | Software R code to apply Stages of Reproductive Aging Workshop + 10 stages to prospectively collected vaginal bleeding data among a cohort of Black women aged 40–55 years. Used to apply STRAW+10 stages to prospectively tracked menstrual bleeding data in a longitudinal cohort study of perimenopausal women. | Stages of Reproductive Aging Workshop, perimenopausal women, prospectively tracked menstrual bleeding data, STRAW+ 10 stages, prospectively collected vaginal bleeding data, | NIMH F32MH134528; NIMH R01MH128244; NINDS T32NS096050 |
PMID:41576711 | Free, Available for download, Freely available | SCR_028698 | 2026-09-05 06:36:17 | 0 | |||||||||
|
CytoVerse Resource Report Resource Website |
CytoVerse (RRID:SCR_028854) | data access protocol, data analysis software, data processing software, data visualization software, software application, software resource, web service | Web application to map single-cell RNA data into AI foundation model spaces. Lets search millions of reference cells and view cell types locally without uploading private data or needing powerful cloud servers. Using ONNX model deployment and compressed IVFPQ indexing, it annotates local datasets against a 23-million-cell reference without server computation, installation, or data upload, and shares embeddings as lightweight files, enabling private, interactive, and collaborative single-cell analysis. | single-cell RNA-seq, foundation models, browser based analysis, WebAssembly, ONNX, scFM, approximate nearest neighbors, latent space collaboration, data privacy, | Brain and Behavior Research Foundation ; California Institute for Regenerative Medicine ; NHGRI RM1HG011543; NIMH U24MH132628; NINDS U24NS146314; NSF ; University of California Office of the President |
PMID:41659670 | Free, Available for download, Freely available | https://github.com/braingeneers/cytoverse | SCR_028854 | 2026-09-05 06:36:20 | 0 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
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.
