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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | data analysis software, data processing software, data visualization software, software application, software resource | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | BAIT - Software to help analyse Strand-Seq data | 2026-09-05 06:24:21 | 1 | |||||
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ARB project Resource Report Resource Website 10+ mentions |
ARB project (RRID:SCR_000515) | ARB | software resource | Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations. | rrna sequence, rrna, phylogeny, alignment, analysis, protein, gene |
is listed by: Debian is related to: SILVA is related to: SINA has parent organization: Technical University of Munich; Bavaria; Germany |
PMID:14985472 | Free, Available for download, Freely available | OMICS_01515 | https://sources.debian.org/src/arb/ | SCR_000515 | The ARB project | 2026-09-05 06:24:22 | 28 | |||||
|
pyQPCR Resource Report Resource Website |
pyQPCR (RRID:SCR_000471) | pyQPCR | software resource | A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu | quantitative pcr, python, qt |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02326 | SCR_000471 | 2026-09-05 06:24:20 | 0 | ||||||||
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RefFinder Resource Report Resource Website 10+ mentions |
RefFinder (RRID:SCR_000472) | RefFinder | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, gene expression, reference gene, web based tool |
uses: BestKeeper uses: NormFinder uses: geNORM is listed by: OMICtools has parent organization: East Carolina University; Carolina; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02321 | http://www.leonxie.com/referencegene.php | SCR_000472 | 2026-09-05 06:24:21 | 45 | |||||||
|
SWORD Resource Report Resource Website 1+ mentions |
SWORD (RRID:SCR_000593) | software resource, web application | A software that is used for the management of data and to deposit content between different locations. A request from an authenticated user is sent to implement for the "service document", which returns details of the collection that user is allowed to deposit within the repository. At this point, the user can deposit their file into a collection, which can then be accessed at a different location. | data storage, deposit content, access, authentication | JISC | Free, Available for download, Freely available | nlx_144633 | SCR_000593 | Simple Web-service Offering Repository Deposit | 2026-09-05 06:24:22 | 1 | ||||||||
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LORIS - Longitudinal Online Research and Imaging System Resource Report Resource Website 1+ mentions |
LORIS - Longitudinal Online Research and Imaging System (RRID:SCR_000590) | LORIS | data management software, software application, software resource | A modular and extensible web-based data management system that integrates all aspects of a multi-center study, from heterogeneous data acquisition to storage, processing and ultimately dissemination, within a streamlined platform. Through a standard web browser, users are able to perform a wide variety of tasks, such as data entry, 3D image visualization and data querying. LORIS also stores data independently from any image processing pipeline, such that data can be processed by external image analysis software tools. LORIS provides a secure web-based and database-driven infrastructure to automate the flow of clinical data for complex multi-site neuroimaging trials and studies providing researchers with the ability to easily store, link, and access significant quantities of both scalar (clinical, psychological, genomic) and multi-dimensional (imaging) data. LORIS can collect behavioral, neurological, and imaging data, including anatomical and functional 3D/4D MRI models, atlases and maps. LORIS also functions as a project monitoring and auditing platform to oversee data acquisition across multiple study sites. Confidentiality during multi-site data sharing is provided by the Subject Profile Management System, which can perform automatic removal of confidential personal information and multiple real-time quality control checks. Additionally, web interactions with the LORIS portal take place over an encrypted channel via SSL, ensuring data security. Additional features such as Double Data Entry and Statistics and Data Query GUI are included. | neuroimaging, multi center, data querying, imaging data, platform, computed tomography, neuroinformatics, 3d, 4d, neurological, imaging, mri model, atlas, map, clinical, image processing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
NICHD N01-HD02-3343; NIMH N01-MH9-0002; NINDS N01-NS-9- 2314; NINDS N01-NS-9-2315; NINDS N01-NS-9-2316; NINDS N01-NS-9-2317; NINDS N01-NS-9- 2319; NINDS N01-NS-9- 2320 |
PMID:22319489 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144608 | http://www.nitrc.org/projects/loris | SCR_000590 | Longitudinal Online Research and Imaging System, Longitudinal Online Research Imaging System | 2026-09-05 06:24:22 | 4 | ||||
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PGS Resource Report Resource Website |
PGS (RRID:SCR_000475) | software resource | Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24947752 | Free, Available for download, Freely available | biotools:pgs, OMICS_04651 | https://bio.tools/pgs | SCR_000475 | PGS: Penalized GEE with Grid Search, Penalized GEE with Grid Search | 2026-09-05 06:24:20 | 0 | ||||||
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Human Disease Ontology Resource Report Resource Website 1+ mentions |
Human Disease Ontology (RRID:SCR_000476) | DO | controlled vocabulary, data or information resource, database, ontology | Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases. | obo, pathological, organismal, cellular, disease, biomedical, health, neurologic disease, neurological disorder, phenotype, bio.tools, |
is used by: DOAF is listed by: BioPortal is listed by: OBO is listed by: bio.tools is listed by: Debian is related to: PharmGKB Ontology is related to: GWASdb is related to: NUgene Project is related to: FunDO is related to: Neurocarta has parent organization: University of Maryland School of Medicine; Maryland; USA |
NHGRI U24 HG012557 | PMID:22080554 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-35926, nlx_157432, SCR_003491, biotools:disease_ontology | http://disease-ontology.org/, https://bio.tools/disease_ontology, http://purl.obolibrary.org/obo/doid.obo, | http://do-wiki.nubic.northwestern.edu/index.php/Main_Page | SCR_000476 | Human Disease Ontology Knowledgebase, Disease Ontology | 2026-09-05 06:24:20 | 5 | |||
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DDBJ Omics Archive Resource Report Resource Website |
DDBJ Omics Archive (RRID:SCR_000597) | DOR | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy. | functional genomics, array, sequence |
is listed by: OMICtools is related to: ArrayExpress is related to: MIAME is related to: MINSEQE is related to: MAGE-TAB has parent organization: DNA DataBank of Japan (DDBJ) |
PMID:22110025 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01026 | http://trace.ddbj.nig.ac.jp/dor | SCR_000597 | Ddbj Omics aRchive | 2026-09-05 06:24:22 | 0 | |||||
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Gazetteer Resource Report Resource Website 1+ mentions |
Gazetteer (RRID:SCR_000473) | GAZ | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available. | obo, owl |
is listed by: BioPortal is listed by: OBO has parent organization: Genomic Standards Consortium |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157412 | http://purl.obolibrary.org/obo/gaz.owl, http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/gaz.obo | http://gensc.org/gc_wiki/index.php/GAZ_Project | SCR_000473 | 2026-09-05 06:24:20 | 1 | ||||||
|
Denver University Department of Psychology Resource Report Resource Website |
Denver University Department of Psychology (RRID:SCR_000474) | data or information resource, department portal, organization portal, portal | The department of psychology at Denver University that offers degrees at the undergraduate, graduate and doctoral level. The doctoral programs have specializations such as Affect/Social, Child Clinical, Cognitive, and Developmental. | psychology, graduate, doctoral, affect, social, child, clinical, cognitive, developmental, neuroscience | has parent organization: University of Denver; Colorado; USA | nif-0000-01928 | SCR_000474 | DU Dept. of Psychology, University of Denver Department of Psychology | 2026-09-05 06:24:20 | 0 | |||||||||
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ContEst Resource Report Resource Website 1+ mentions |
ContEst (RRID:SCR_000595) | ContEst | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data. | java, contamination, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:21803805 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01038, biotools:contest | https://bio.tools/contest | SCR_000595 | 2026-09-05 06:24:22 | 6 | ||||||
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ECNP Resource Report Resource Website 1+ mentions |
ECNP (RRID:SCR_000501) | ECNP | community building portal, data or information resource, portal | A pan-European scientific association to encourage research across the neurosciences and to translate new knowledge on fundamental disease mechanisms into new medicines and clinical applications. As an interdisciplinary forum for the science and treatment of disorders of the brain, they promote the communication and cross- fertilization of high-quality experimental and clinical research across the field of neuroscience. ECNP is a non-profit member-based association, independently governed and self-funded. ECNP is a public-interest-serving entity. | brain, neuroscience, disease mechanism, medicine, clinical, disease | is parent organization of: Preclinical Data Forum Network | Brain disorder | nlx_158605 | SCR_000501 | European College of Neuropsychopharmacology, ECNP - neuroscience applied | 2026-09-05 06:24:22 | 1 | |||||||
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SpeedSeq Resource Report Resource Website 1+ mentions |
SpeedSeq (RRID:SCR_000469) | software resource | Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)). | standalone software |
is listed by: OMICtools has parent organization: University of Virginia; Virginia; USA |
Free, Available for download, Freely available | OMICS_04673 | SCR_000469 | 2026-09-05 06:24:20 | 7 | |||||||||
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Health Level Seven International Resource Report Resource Website |
Health Level Seven International (RRID:SCR_000466) | HL7 | institution | ANSI-accredited standards developing organization providing a comprehensive framework and related standards for the exchange, integration, sharing, and retrieval of electronic health information that supports clinical practice and the management, delivery and evaluation of health services. HL7's 2,300+ members include approximately 500 corporate members who represent more than 90% of the information systems vendors serving healthcare. HL7 provides standards for interoperability that improve care delivery, optimize workflow, reduce ambiguity and enhance knowledge transfer among all of their stakeholders, including healthcare providers, government agencies, the vendor community, fellow SDOs and patients. | health care, interoperability, health, health service, clinical, management | is parent organization of: Health Level Seven Reference Implementation Model Version 3 | nlx_157307, Wikidata: Q17054989, grid.434932.b | https://ror.org/029ga8k16 | SCR_000466 | 2026-09-05 06:24:20 | 0 | ||||||||
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MPscan Resource Report Resource Website |
MPscan (RRID:SCR_000587) | MPscan | data access protocol, software resource, web service | Web tool for index free mapping of multiple short reads on a genome. | linux, macos, next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ATGC: Montpellier bioinformatics platform |
Free, Available for download, Freely available | biotools:mpscan, OMICS_00670 | https://bio.tools/mpscan | SCR_000587 | MPscan: index free mapping of multiple short reads on a genome | 2026-09-05 06:24:22 | 0 | ||||||
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FluWikie.com Resource Report Resource Website |
FluWikie.com (RRID:SCR_000506) | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Flu Wikie is a topical portal on the flu. Major categories include health, Flu Symptoms, Avian Influenza, Swine Flu, Cold, Vaccination, Pandemic, Vitamin D, and Immune System. Many articles on topic are included. | virus | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_22823 | SCR_000506 | Flu Wikie, FluWikie | 2026-09-05 06:24:21 | 0 | |||||||||
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MATCHCLIP Resource Report Resource Website |
MATCHCLIP (RRID:SCR_000541) | MATCHCLIP | software resource | Software program that detects the precise break points of Copy number variations (CNVs) through a fuzzy string matching algorithm using both CIGAR and POS information. In case the two break points of a CNV are in repeated regions and the break points are not unique, it reports the range where the break points can slide. | breakpoint, deletion, duplication, exon sequencing, structural variation, next generation sequencing |
is listed by: OMICtools has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
PMID:23967014 | Free, Available for download, Freely available, | OMICS_02289 | SCR_000541 | matchclips2, MATCHCLIPS | 2026-09-05 06:24:21 | 0 | ||||||
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Exonhit Therapeutics Resource Report Resource Website |
Exonhit Therapeutics (RRID:SCR_000493) | commercial organization | A drug and diagnostic discovery company. | drug, diagnostic, in vitro | is related to: PharmaCog | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158329 | SCR_000493 | Diaxonhit, Exonhit Therapeutics SA, ExonHit Therapeutics S.A. | 2026-09-05 06:24:20 | 0 | ||||||||
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TDARACNE Resource Report Resource Website |
TDARACNE (RRID:SCR_000498) | TDARACNE | software resource | Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data. | microarray, time course |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02013 | SCR_000498 | TDARACNE - Network reverse engineering from time course data | 2026-09-05 06:24:21 | 0 |
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