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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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LIGER Resource Report Resource Website 10+ mentions |
LIGER (RRID:SCR_018100) | software application, data processing software, data analysis software, software resource | Software R package for integrating and analyzing multiple single-cell datasets. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. Used for analysis of multiple scRNA-seq data sets. | Single cell genomic, data integration, dataset, cell identity, integrative analysis, gene regulation, disease state, scRNA seq analysis, shared factor among data set, | has parent organization: Broad Institute | NIH | PMID:31178122 | Free, Available for download, Freely available | https://github.com/MacoskoLab/liger | SCR_018100 | Linked Inference of Genomic Experimental Relationships | 2026-02-15 09:21:32 | 12 | ||||||
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Data and Computational Resources to Address COVID-19 Resource Report Resource Website |
Data and Computational Resources to Address COVID-19 (RRID:SCR_018274) | disease-related portal, topical portal, data or information resource, portal | COVID-19 open access data and computational resources provided by federal agencies, including NIH, public consortia, and private entities. Continuously updated as more information becomes available. These resources are being shared for scientific and public health interests, and content is responsibility of resource organizers. | COVID-19, COVID-19 data, federal agency data, computational resource, public health information, SARS-CoV-2, NIH |
lists: Nextstrain lists: outbreak.info lists: Research Data Alliance Working Group lists: UC Health clinical data warehouse lists: Vivli lists: Cloud resources for COVID-19 research lists: COVID-19 High Performance Computing Consortium lists: Data-Against-COVID Team lists: NASEM Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats lists: NIAID Overview of Coronaviruses lists: Schema.org lists: Virus Pathogen Resource (ViPR) lists: Modeling Infectious Disease Agents Study online portal for COVID-19 lists: LitCovid lists: Broad Terra cloud commons for pathogen surveillance lists: COVID-19 research data on Figshare lists: Dimensions COVID-19 publications, datasets and clinical trials lists: COVID-19 Open Research Dataset lists: Global Initiative on Sharing All Influenza Data |
COVID-19 | NIH | Free, Freely available | SCR_018817 | SCR_018274 | Open Access Data and Computational Resources to Address COVID-19, NIH Open-Access Data and Computational Resources to Address COVID-19 | 2026-02-15 09:22:20 | 0 | ||||||
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GLYCAM-Web Resource Report Resource Website 50+ mentions |
GLYCAM-Web (RRID:SCR_018260) | portal, software resource, data access protocol, web service, data or information resource, topical portal | Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates. | Glycosylated SARS-Cov-2 Spike protein, SARS-Cov-2, SARS-Cov-2 Spike protein, spike protein, 3D structure, carbohydrate, oligosaccharide conformation, modeling, structure modeling, data | has parent organization: University of Georgia; Georgia; USA | COVID-19, COVID19 | NIH | Free, Freely available | SCR_018260 | GLYCAM | 2026-02-15 09:22:12 | 96 | |||||||
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Multi-omics Visualization Platform Resource Report Resource Website 1+ mentions |
Multi-omics Visualization Platform (RRID:SCR_018077) | MVP | software application, data visualization software, data processing software, software resource, data analysis software | Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach. | Proteogenomics, data, multi-omics, mass spectrometry, proteomics, genomics, transcriptomics, Galaxy Project, data visualization, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIH U24 CA199347 | Free, Available for download, Freely available | biotools:mvp_a | http://galaxyp.org https://bio.tools/mvp_a |
SCR_018077 | Multi-omics Visualization Platform, Galaxy MVP | 2026-02-15 09:22:10 | 1 | |||||
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NIH COVID-19 Portfolio Resource Report Resource Website 10+ mentions |
NIH COVID-19 Portfolio (RRID:SCR_018295) | software resource, data access protocol, web service, service resource, data or information resource | NIH comprehensive, curated source for publications related to COVID-19. Includes articles from PubMed and pre-prints from arXiv, medRxiv, bioRxiv, and ChemRxiv. Updated daily. NIH Office of Portfolio Analysis has developed this resource to explore and analyze set of advances in COVID‑19 research as they accumulate in real time, and complements efforts by NLM to aggregate full text documents broadly related to COVID-19 and other outbreaks, and articles on COVID‑19 specific to PubMed database. | COVID-19 publication, COVID-19 article, COVID-19 data, COVID-19 full text document, COVID-19 pre-print | COVID-19 | NIH | Free, Freely available | SCR_018295 | iSearch COVID-19 portfolio, COVID-19 Portfolio Tool From the Office of Portfolio Analysis, iSearch COVID-19 Portfolio, COVID-19 Portfolio | 2026-02-15 09:22:12 | 17 | ||||||||
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TeamTat Resource Report Resource Website 1+ mentions |
TeamTat (RRID:SCR_023439) | web application, software resource | Web based collaborative text annotation tool. Used for managing multi-user, multi-label document annotation. Project managers can specify annotation schema for entities and relations and select annotators and distribute documents anonymously to prevent bias. Document input format can be plain text, PDF or BioC (uploaded locally or automatically retrieved from PubMed/PMC), and output format is BioC with inline annotations. Displays figures from full text. | Text annotation, team collaboration, collaborative text annotation, | MSIT ; NIH |
PMID:32383756 | Free, Freely available | https://github.com/ncbi-nlp/TeamTat | SCR_023439 | 2026-02-15 09:23:10 | 3 | ||||||||
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Dynamic Regulatory Events Miner Resource Report Resource Website 1+ mentions |
Dynamic Regulatory Events Miner (RRID:SCR_003080) | DREM | software application, data processing software, software resource | The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations | transcription, gene regulation, dynamics, time series, gene expression, static, dynamic, transcription factor-gene interaction, chip-chip, transcription factor, regulatory network, hidden markov model, systems biology, gene regulatory network, times series expression data, dynamic network, chip-seq | has parent organization: Carnegie Mellon University; Pennsylvania; USA | NIH ; NIGMS 1RO1 GM085022; NIAID DNO1 AI-5001; NSF 0448453 |
PMID:22897824 | Free, Available for download, Freely available | nif-0000-30478 | SCR_003080 | Dynamic Regulatory Events Miner (DREM) | 2026-02-15 09:18:26 | 5 | |||||
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Roadmap Resource Report Resource Website 10+ mentions |
Roadmap (RRID:SCR_017207) | software application, software resource | Software tool to display surface of macromolecule and its properties. Uses projections to map van der Waals or solvent accessible surface of macromolecule onto plane., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Display, surface, macromolecule, property, projection, van der Waal | is related to: Purdue University; West Lafayette; Indiana | NSF ; NIH ; Medical Research Council |
PMID:8384042 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017207 | 2026-02-15 09:21:59 | 14 | ||||||||
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Conservation Resource Report Resource Website 1000+ mentions |
Conservation (RRID:SCR_016064) | software application, software toolkit, software resource | Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands. | scoring, protein, sequence, conservation, Jensen-Shannon, divergence, predict, catalytic, site, bound, ligands, clustal, fasta, concave | is related to: Princeton University; New Jersey; USA | NIH T32 HG003284; NSF IIS-0612231; NSF PECASE MCB-0093399; NIGMS GM076275; NIH P50 GM071508 |
PMID:17519246 | Free, Available for download | SCR_016064 | Conservation-code | 2026-02-15 09:21:01 | 1564 | |||||||
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GlimmerHMM Resource Report Resource Website 500+ mentions |
GlimmerHMM (RRID:SCR_002654) | GlimmerHMM | source code, software resource | A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single). | gene, hidden markov model |
is related to: Glimmer has parent organization: Johns Hopkins University; Maryland; USA |
NIH ; NLM R01-LM06845; NLM R01-LM007938 |
PMID:15145805 | Free, Available for download, Freely available | nlx_156092 | SCR_002654 | GlimmerHMM - Eukaryotic Gene-Finding System | 2026-02-15 09:18:22 | 576 | |||||
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neurospy Resource Report Resource Website |
neurospy (RRID:SCR_007016) | neurospy | source code, software resource | neurospy is a free software for functional imaging of fast neuronal activity. neurospy is a modular cross-platform application framework written in Java for the NetBeans Platform. At this time it runs on Windows XP-based LeCroy oscilloscopes and drives acousto-optic scanners via USB using the Analog Devices 9959 Direct Digital Synthesis chip. This combination makes one of the most powerful systems for scanning microscopy available today at any price. neurospy is very easy to port to other kinds of acquisition and scanning hardware. | imaging, neuron, microscopy, functional imaging, java, neuronal activity |
has parent organization: SourceForge has parent organization: Howard Hughes Medical Institute has parent organization: Salk Institute for Biological Studies has parent organization: University of California at San Diego; California; USA |
Howard Hughes Medical Institute ; NIH |
PMID:17684546 | Open unspecified license | nlx_149367 | SCR_007016 | 2026-02-15 09:19:25 | 0 | ||||||
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vhlab-microscopyimageanalysis-matlab Resource Report Resource Website 1+ mentions |
vhlab-microscopyimageanalysis-matlab (RRID:SCR_024450) | software application, source code, software resource | Software Matlab app for analysis of high density imaging data like that from Array Tomography. | Matlab, array tomography, super-resolution imaging, high density imaging data, high density imaging data analysis, | NIH | Free, Available for download, Freely available | SCR_024450 | 2026-02-15 09:23:32 | 1 | ||||||||||
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Bio-Synthesis Resource Report Resource Website 100+ mentions |
Bio-Synthesis (RRID:SCR_000820) | material resource, biomaterial supply resource | A commercial supplier of custom synthetic molecules. They specialize in peptides, oligonucleotides, bioconjugation, molecular biology services, proteins and specialty chemistry. | antibody, synthetic molecule, peptides, oligonucleotide, bioconjugation, protein | is listed by: ScienceExchange | NIH 263-00050713-01 | nlx_152297, SciEx_516 | SCR_000820 | Bio-Synthesis Inc. | 2026-02-15 09:17:59 | 167 | ||||||||
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Midas Platform Resource Report Resource Website 10+ mentions |
Midas Platform (RRID:SCR_002186) | Midas | data management software, software application, software toolkit, software resource | Open-source toolkit that enables the rapid creation of tailored, web-enabled data storage and provides a cohesive system for data management, visualization, and processing. At its core, Midas Platform is implemented as a PHP modular framework with a backend database (PostGreSQL, MySQL and non-relational databases). While the Midas Platform system can be installed and deployed without any customization, the framework has been designed with customization in mind. As building one system to fit all is not optimal, the framework has been extended to support plugins and layouts. Through integration with a range of other open-source toolkits, applications, or internal proprietary workflows, Midas Platform offers a solid foundation to meet the needs of data-centric computing. Midas Platform provides a variety of data access methods, including web, file system and DICOM server interfaces, and facilitates extending the methods in which data is stored to other relational and non-relational databases. | data storage, data analysis, visualization, multimedia, digital archiving, processing | has parent organization: Kitware | NLM ; NIH ; NCI |
PMID:18560078 | Apache License, v2, Simplified BSD License, BSD License | nlx_154696 | SCR_002186 | Midas Platform - The Multimedia Digital Archiving System | 2026-02-15 09:18:15 | 42 | |||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | software application, data processing software, software resource, software toolkit, data analysis software | Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations. | analysis, heterogenous, population, single, cell, gene, expression, data, large, single-cell RNA-Seq, transcriptional, regulation, heterogen | NIH DP2 HD088158; Alfred P. Sloan Foundation Research Fellowship |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-02-15 09:21:05 | 203 | ||||||||
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MAST Resource Report Resource Website 50+ mentions |
MAST (RRID:SCR_016340) | MAST | software application, data processing software, software resource, software toolkit, data analysis software | Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. | model, based, analysis, single, cell, transcriptomics, RNA, sequencing, data | NIH DP2 DE023321; NIBIB R01 EB008400; Bill and Melinda Gates Foundation OPP1032317 |
DOI:10.5281/zenodo.18539 | Free, Available for download, Freely available | https://github.com/RGLab/MAST/ | SCR_016340 | Model based Analysis of Single Cell Transcriptomics | 2026-02-15 09:21:38 | 86 | ||||||
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NIAID Resource Report Resource Website 500+ mentions |
NIAID (RRID:SCR_016598) | NIAID | organization portal, portal, data or information resource, topical portal, disease-related portal | National Institute of Allergy and Infectious Diseases is a leading research institution to understand, treat, and prevent infectious, immunologic, and allergic diseases. | immunologic, allergic, infectious, disease, institute, treat, prevent |
lists: Nephele lists: PaVE lists: ChemokineDB lists: SPICE lists: TRIAGE lists: NGlycPred lists: dCAS lists: HASP lists: ABC Bacterial Transporter Systems Database lists: TB PORTALS lists: JOINSOLVER is related to: The Immunology Database and Analysis Portal (ImmPort) is related to: The 10000 Immunomes is related to: NIAID Overview of Coronaviruses is parent organization of: OMiCC is parent organization of: OCICB is parent organization of: NetCirChro |
NIH | SCR_016598 | National Institute of Allergy and Infectious Diseases | 2026-02-15 09:21:45 | 510 | ||||||||
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SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | software application, data visualization software, data processing software, software resource, data analysis software | Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically. | data, mining, visualization, analysis, polychromatic, flow, cytometry, dataset, normalized, graphically, bio.tools |
is listed by: NIAID is listed by: Debian is listed by: bio.tools |
NIAID ; NIH |
PMID:21265010 | Free, Available for download, Freely available | biotools:spice | https://bio.tools/spice | SCR_016603 | Simplified Presentation of Incredibly Complex Evaluations | 2026-02-15 09:21:45 | 66 | ||||
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Cleveland Family Study Resource Report Resource Website 1+ mentions |
Cleveland Family Study (RRID:SCR_016585) | CFS | disease-related portal, topical portal, data or information resource, portal | Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore. | data, polysomnography, sleep apnea, family, familial aggregation, EEG, ECG, longitudinal | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | NHLBI HL46380; NHLBI T32 HL07567; NIH R01 46380; NCRR M01 RR00080 |
PMID:7881656 | SCR_016585 | Cleveland Family Study | 2026-02-15 09:21:44 | 3 | ||||||
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MAxEntScan Resource Report Resource Website 50+ mentions |
MAxEntScan (RRID:SCR_016707) | MAxEntScan | software application, simulation software, service resource, software resource | Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing. | modeling, sequence, short, motif, maximum, entropy, principle, MEP, RNA, splicing |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
NSF Grant 0218506; NIH ; Lee Kuan Yew Scholarship for the goverment of Singapore |
PMID:15285897 | Free, Available for download, Freely available | SCR_016707 | Maximum Entropy Scan, MAxEntScan, MAximumEntropyScan | 2026-02-15 09:21:47 | 65 |
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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.
