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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
LRPath Resource Report Resource Website 1+ mentions |
LRPath (RRID:SCR_018572) | data access protocol, production service resource, analysis service resource, service resource, software resource, web service | Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. | Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIEHS P30 ES06096; NIEHS U01 ES015675; NHGRI R01 HG003749; NLM R01 LM008106; NIDA U54 DA021519 |
PMID:19038984 | Free, Freely available | biotools:lrpath | https://bio.tools/lrpath | SCR_018572 | 2026-02-17 10:03:07 | 4 | ||||||
|
Limitation-Recognizer Resource Report Resource Website |
Limitation-Recognizer (RRID:SCR_018747) | data analysis software, software application, data processing software, software resource | Software tool to recognize self acknowledged limitation sentences in biomedical articles. Automatic recognition of self acknowledged limitations in clinical research literature to support efforts in improving research transparency. | ASWG, automatic recognition, self acknowledged limitation, clinical research literature, research transparency, limitation sentence recognition |
uses: Stanford CoreNLP has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NLM | PMID:29718377 | Free, Freely available | SCR_018748 | SCR_018747 | limitationrecognizer, limitation recognizer, limitation-recognizer | 2026-02-17 10:03:48 | 0 | ||||||
|
ANTIGENpro Resource Report Resource Website 100+ mentions |
ANTIGENpro (RRID:SCR_018779) | data access protocol, service resource, web service, software resource | 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 | NLM LM 07443; NSF EIA 0321390; NSF 0513376; Microsoft Faculty Research Award |
PMID:20934990 | Free, Freely available | SCR_018779 | 2026-02-17 10:03:51 | 247 | ||||||||
|
fMRIPrep Resource Report Resource Website 1000+ mentions |
fMRIPrep (RRID:SCR_016216) | image processing software, software application, data processing software, 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 RL1 MH083268; NIMH RL1 MH083269; NIMH RL1 DA024853; NIMH RL1 MH083270; NIMH PL1 MH083271; NLM RL1 LM009833; NINDS PL1 NS062410 |
PMID:30532080 PMID:32514178 |
Free, Available for download, Freely available | https://zenodo.org/record/1219187#.WuDlO4jwZPY | SCR_016216 | fMRIPrep, FMRI PREP | 2026-02-17 10:02:40 | 1190 | ||||||
|
lilikoi Resource Report Resource Website 1+ mentions |
lilikoi (RRID:SCR_016361) | software application, data processing software, data analysis software, 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 |
NIEHS K01 ES025434; NIGMS GM103457; NLM R01 LM012373; NICHD R01 HD084633 |
DOI:https://doi.org/10.1101/283408 | Free, Available for download, Freely available | https://omictools.com/lilikoi-tool | SCR_016361 | 2026-02-17 10:02:41 | 3 | |||||||
|
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 | 2026-02-17 10:04:23 | 2 | ||||||||
|
Midas Platform Resource Report Resource Website 10+ mentions |
Midas Platform (RRID:SCR_002186) | Midas | data management software, software application, software resource, software toolkit | 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 | 2026-02-17 09:59:51 | 42 | |||||
|
The NINDS Human Cell and Data Repository (NHCDR) Resource Report Resource Website 10+ mentions |
The NINDS Human Cell and Data Repository (NHCDR) (RRID:SCR_016319) | NHCDR | biomaterial supply resource, tissue bank, material resource | Cell sources currently include fibroblasts and/or induced pluripotent stem cells for Alzheimer's Disease, Amyotrophic Lateral Sclerosis (ALS), Ataxia-telangiectasia, Frontotemporal Lobar Degeneration (FTD), Huntington's Disease, Parkinson's Disease, and healthy controls. Cell sources, including isogenic cell lines for current and new diseases covered by the NINDS will be added over the next several years. | Stem, cell, fibroblast, plutipotent, isogenic |
is used by: NIH Heal Project is recommended by: National Library of Medicine is listed by: re3data.org works with: Cellosaurus |
Alzheimer's Disease, Amyotrophic Lateral Sclerosis (ALS), Ataxia-telangiectasia, Frontotemporal Lobar Degeneration (FTD), Huntington's Disease, Parkinson's Disease | NLM ; NINDS |
Restricted | https://nindsgenetics.org/ | SCR_016319 | NINDS Human Cell and Data Repository (NHCDR) | 2026-02-17 10:02:41 | 16 | |||||
|
CDEMapper Resource Report Resource Website |
CDEMapper (RRID:SCR_027602) | software application, source code, software resource | 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 | 2026-02-17 10:04:47 | 0 |
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