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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ANTIGENpro Resource Report Resource Website 100+ mentions |
ANTIGENpro (RRID:SCR_018779) | data access protocol, service resource, software resource, web service | Web tool as sequence-based, alignment-free and pathogen-independent predictor of protein antigenicity.Predicts likelihood that protein is protective antigen. Integrated in SCRATCH suite of predictors. | Protein antigenicity, sequence based predictior, alignment free predictor, pathogen independent predictor, protein antigenicity predictor, SCRATCH suite, predictor | has parent organization: University of California at Irvine; California; USA | Microsoft Faculty Research Award ; NLM LM 07443; NSF 0513376; NSF EIA 0321390 |
PMID:20934990 | Free, Freely available | SCR_018779 | 2026-09-12 12:59:06 | 343 | ||||||||
|
DeepCell Resource Report Resource Website 10+ mentions |
DeepCell (RRID:SCR_022197) | data processing software, image analysis software, segmentation software, software application, software resource | Software for segmenting individual cells in microscopy images using deep learning. Cell segmentation software. | segmenting individual cells, microscopy image, cell segmentation | NIGMS F32 GM119319; NIGMS P50 GM107615; NLM DP1 LM01150; Paul Allen Family Foundation |
DOI:10.1371/journal.pcbi.1005177 | Free, Available for download, Freely available | SCR_022197 | Deepcell | 2026-09-12 01:00:06 | 14 | ||||||||
|
Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions Resource Report Resource Website |
Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (RRID:SCR_017140) | HIBACHI, hibachi | simulation software, software application, software resource | Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods. | data, simulation, dataset, compare, machine, evaluate, learning, method | NIAID AI116794; NIDDK DK112217; NLM LM012601 |
PMID:29218887 | Free, Available for download, Freely available | SCR_017140 | Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions | 2026-09-12 12:58:49 | 0 | |||||||
|
fMRIPrep Resource Report Resource Website 1000+ mentions |
fMRIPrep (RRID:SCR_016216) | data processing software, image processing software, software application, software resource | Software tool as robust preprocessing pipeline for functional MRI.Used for preprocessing of diverse fMRI data. | Processing data, fmri, neuroimaging, coregistration, normalization, unwarping, noise, component, extraction, segmentation, skullstripping |
uses: Nipype has parent organization: Poldracklab Portal works with: NiPoppy |
Laura and John Arnold Fundation ; NIDCR UL1 DE019580; NIMH PL1 MH083271; NIMH RL1 DA024853; NIMH RL1 MH083268; NIMH RL1 MH083269; NIMH RL1 MH083270; NINDS PL1 NS062410; NLM RL1 LM009833 |
PMID:30532080 PMID:32514178 |
Free, Available for download, Freely available | https://zenodo.org/record/1219187#.WuDlO4jwZPY | SCR_016216 | fMRIPrep, FMRI PREP | 2026-09-12 12:58:36 | 1457 | ||||||
|
lilikoi Resource Report Resource Website 1+ mentions |
lilikoi (RRID:SCR_016361) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction. | personalized, medicine, metabolomics, data, classification, clustering, biomarker, prediction, algorithm, calculating, microarray, enrichment |
is listed by: OMICtools is related to: University of Hawaii; Hawaii; USA |
NICHD R01 HD084633; NIEHS K01 ES025434; NIGMS GM103457; NLM R01 LM012373 |
DOI:https://doi.org/10.1101/283408 | Free, Available for download, Freely available | https://omictools.com/lilikoi-tool | SCR_016361 | 2026-09-12 12:58:38 | 3 | |||||||
|
SHRINE Resource Report Resource Website 1+ mentions |
SHRINE (RRID:SCR_006293) | SHRINE | software application, software resource, source code | Software providing a scalable query and aggregation mechanism that enables federated queries across many independently operated patient databases. This platform enables clinical researchers to solve the problem of identifying sufficient numbers of patients to include in their studies by querying across distributed hospital electronic medical record systems. Through the use of a federated network protocol, SHRINE allows investigators to see limited data about patients meeting their study criteria without compromising patient privacy. This software should greatly enable population-based research, assessment of potential clinical trials cohorts, and hypothesis formation for followup study by combining the EHR assets across the hospital system. In order to obtain the maximum number of cases representing the study population, it is useful to aggregate patient facts across as many sites as possible. Cutting across institutional boundaries necessitates that each hospital IRB remain in control, and that their local authority is recognized for each and every request for patient data. The independence, ownership, and legal responsibilities of hospitals predetermines a decentralized technical approach, such as a federated query over locally controlled databases. The application comes with the SHRINE Core Ontology but it can be used with any ontology, even one that is disease specific. The Core Ontology is designed to enable the widest range of studies possible using facts gathered in the EMR during routine patient care. SHRINE allows multiple ontologies to be used for different research purposes on the same installed systems. | software network, clinical database, data sharing, clinical, medical record, federated, platform, network |
is related to: i2b2 Cross-Institutional Clinical Translational Research project is related to: i2b2 Research Data Warehouse has parent organization: Harvard Medical School; Massachusetts; USA |
Informatics for Integrating Biology and the Bedside ; NLM 5 U54 LM008748; NCRR 1 UL1 RR025758-01 |
PMID:19567788 | Available under a BSD3 Open unspecified license Software license. | nlx_151949 | SCR_006293 | Shared Health Research Informatics NEtwork | 2026-09-12 01:01:42 | 8 | |||||
|
GlimmerHMM Resource Report Resource Website 500+ mentions |
GlimmerHMM (RRID:SCR_002654) | GlimmerHMM | software resource, source code | 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 | 2026-09-12 01:03:13 | 643 | |||||
|
tTFtarget Resource Report Resource Website 1+ mentions |
tTFtarget (RRID:SCR_025631) | data or information resource, database | Transcription factor target database. Platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments and target genes or transcripts across multiple organisms. | Transcription factor target, validated binding sites, transfer RNA-derived fragments, target genes, multiple organisms, | NLM R01LM014087; NSF |
DOI:10.1093/nar/gkad815 | Free, Freely available | SCR_025631 | tRFtarget 2.0, tRFtarget 1.0 | 2026-09-12 01:04:48 | 4 | ||||||||
|
RFMix Resource Report Resource Website 1+ mentions |
RFMix (RRID:SCR_027030) | software application, software resource | Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference. | Discriminative Modeling, local ancestry and admixture inference, | NHGRI 2R01HG003229; NLM LM007033; NSF |
PMID:23910464 | Restricted | SCR_027030 | 2026-09-12 01:05:17 | 9 | |||||||||
|
CDEMapper Resource Report Resource Website |
CDEMapper (RRID:SCR_027602) | software application, software resource, source code | Software Common Data Elements (CDEs) mapping tool to bridge the gap between local data elements and National Institutes of Health (NIH) CDEs. Elasticsearch and Large Language Model (LLM)-powered mapping tool designed for biomedical and clinical researchers to efficiently map study variables to the NIH Common Data Elements (CDEs). It integrates essential and advanced services into a user-centered mapping workflow, allowing users to choose different mapping strategies based on their project's needs.Used for enhancing National Institutes of Health common data element use with large language models. | mapping, map study variables, NIH Common Data Elements, map study variables to NIH Common Data Elements, | NLM U24LM013755 | PMID:40332956 | Free, Available for download, Freely available | https://github.com/BIDS-Xu-Lab/CDE-Mapping-Tool | SCR_027602 | CDEMapper 2.0 | 2026-09-12 01:05:31 | 0 |
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