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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TMAJ Resource Report Resource Website 10+ mentions |
TMAJ (RRID:SCR_005601) | TMAJ | software resource | Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program. | tissue microarray, java, java swing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA has parent organization: SourceForge |
GNU General Public License, v3 | biotools:tmaj, OMICS_00823 | https://bio.tools/tmaj | SCR_005601 | TMAJ Software Project | 2026-02-14 02:00:56 | 10 | ||||||
|
GOProfiler Resource Report Resource Website 1+ mentions |
GOProfiler (RRID:SCR_005683) | GOProfiler | service resource | Service that provides a summary of GO annotations available for each species. The user provides a taxon id and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided. | ontology or annotation browser, annotation, protein, gene ontology |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: AgBase |
PMID:16961921 | Free for academic use | OMICS_02269, nlx_149127 | SCR_005683 | 2026-02-14 02:00:59 | 2 | |||||||
|
National Hellenic Research Foundation Resource Report Resource Website 1+ mentions |
National Hellenic Research Foundation (RRID:SCR_005719) | NHRF | institution | The National Hellenic Research Foundation (NHRF) is a multidisciplinary Research Centre established by Royal Decree on 9th October 1958. Its purpose is the organisation, finance and support of high-level research projects in the humanities and the natural sciences. The Humanities Institute cover a wide spectrum of study and research fields in Greek history and culture, contributing substantially and critically to the knowledge and promotion of Greek identity. The Natural Sciences Institutes perform basic and applied research in leading edge areas of science such as health, pharmaceuticals, environment, biotechnology and new materials. They develop innovative methods for solving complex problems facing Greek industry and they provide specialised services and know-how both to the public and private sector. The NHRF is governed by the Board of Directors and the Central Administration under the Director/Chairman of the Board. | humanities, natural sciences | is parent organization of: StRAnGER | ISNI: 0000 0001 2232 6894, grid.22459.38, Wikidata: Q1248816, nlx_149177 | https://ror.org/033m02g29 | SCR_005719 | National Hellenic Research Foundation | 2026-02-14 02:01:09 | 4 | |||||||
|
Stanford TMA Software Resource Report Resource Website 1+ mentions |
Stanford TMA Software (RRID:SCR_005598) | Stanford TMA | software resource | Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays. | tissue microarray |
is listed by: OMICtools is related to: TMA-Combiner has parent organization: Stanford University; Stanford; California |
PMID:12414504 | OMICS_00819 | SCR_005598 | Stanford TMA Software website, Stanford Tissue Microarray Software | 2026-02-14 02:00:58 | 1 | |||||||
|
OXBench Resource Report Resource Website 1+ mentions |
OXBench (RRID:SCR_005591) | OXBench | software resource | A suite of programs aimed at developers of alignment methods rather than end-users to assess the accuracy of multiple sequence alignment methods. It includes a reference database of protein multiple sequence alignments that were generated by consideration of protein three-dimensional structure. | alignment, linux, protein, sequence alignment |
is listed by: OMICtools has parent organization: University of Dundee; Scotland; United Kingdom |
PMID:14552658 | Acknowledgement requested | OMICS_00983 | http://www.compbio.dundee.ac.uk/Software/Oxbench/oxbench.html Alt. URL: http://www.compbio.dundee.ac.uk/software.html | SCR_005591 | 2026-02-14 02:00:57 | 2 | ||||||
|
Staden Package Resource Report Resource Website 50+ mentions |
Staden Package (RRID:SCR_005629) | software resource | A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. | c, unix/linux, sequence assembly, dna/protein analysis, spin, sequence alignment, genome, genome viewer, c++, fortran, tcl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20513662 DOI:10.1093/bioinformatics/btq268 |
BSD License | OMICS_00894, biotools:staden | https://bio.tools/staden https://sources.debian.org/src/staden/ |
SCR_005629 | Staden Package | 2026-02-14 02:01:09 | 79 | ||||||
|
Chromaseq Resource Report Resource Website 1+ mentions |
Chromaseq (RRID:SCR_005587) | Chromaseq | software resource | A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap. | chromatogram, sequence, mesquite |
is listed by: OMICtools has parent organization: Oregon State University; Oregon; USA |
NSF EF-0531754 | Acknowledgement required | OMICS_01017 | SCR_005587 | Chromaseq: a package for processing chromatograms and sequence data in Mesquite | 2026-02-14 02:01:09 | 7 | ||||||
|
snp-search Resource Report Resource Website |
snp-search (RRID:SCR_005618) | snp-search | software resource | A software tool that manages SNP data and outputs useful information which can be used to test important biological hypotheses. | is listed by: OMICtools | PMID:24246037 | OMICS_00303 | SCR_005618 | 2026-02-14 02:00:56 | 0 | |||||||||
|
Chung-Ang University; Seoul; South Korea Resource Report Resource Website |
Chung-Ang University; Seoul; South Korea (RRID:SCR_003547) | university | Private comprehensive research university in South Korea. Starting as a church-run kindergarten in 1918, CAU transformed into a school for female kindergarten teachers in 1922 and was granted university status in 1953. | grid.254224.7, ISNI:0000 0001 0789 9563, Crossref funder ID:501100002460, nlx_10442, Wikidata:Q41790 | https://ror.org/01r024a98 | SCR_003547 | CAU | 2026-02-14 02:00:28 | 0 | ||||||||||
|
MAGENTA Resource Report Resource Website 100+ mentions |
MAGENTA (RRID:SCR_003422) | MAGENTA | software resource | A computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes, using genome-wide genetic data as input. |
is listed by: OMICtools has parent organization: Broad Institute |
PMID:20714348 | Free, Available for download, Freely available | OMICS_00236 | SCR_003422 | Meta-Analysis Gene-set Enrichment of variaNT Associations | 2026-02-14 02:00:27 | 140 | |||||||
|
NAPPA Resource Report Resource Website 10+ mentions |
NAPPA (RRID:SCR_003419) | NAPPA | software resource | Software that enables the processing and normalization of the standard mRNA data output from the Nanostring nCounter software. | normalization, processing, nanostring, mirna, mrna, os x, windows | is listed by: OMICtools | GNU General Public License, v3 | OMICS_02310 | SCR_003419 | NAPPA: Performs the processing and normalisation of Nanostring miRNA and mRNA data | 2026-02-14 02:00:48 | 12 | |||||||
|
FadE Resource Report Resource Website 10+ mentions |
FadE (RRID:SCR_003448) | FadE | software resource | A software package designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer or nucleotide reads produced by the Illumina or 454 sequencing platforms. |
is listed by: OMICtools has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:22965123 | Free, Available for download, Freely available | OMICS_00599 | https://minituba.hegroup.org/ | SCR_003448 | fade - Estimation of position specific methylation parameters in color or nucleotide space with NR optimization | 2026-02-14 02:00:27 | 34 | ||||||
|
Proteome Commons Tranche repository Resource Report Resource Website 1+ mentions |
Proteome Commons Tranche repository (RRID:SCR_003441) | Tranche | software resource | A distributed file storage system that you can upload files to and download files from. All files uploaded to the repository are replicated several times to protect against their accidental loss. Files uploaded to the repository can be of any size, can be of any file type, and can be encrypted with a passphrase of your choosing. The Proteome Commons Tranche repository is the first instance of a Tranche repository. Tranche, was created so that anybody can take it and make their own Tranche repository. This is the first implementation of the Tranche software, and is useful as a test bed for the software. This repository relies on educational institutions to provide the hardware and facilities for Tranche servers. While we maintain a set of servers, the continued growth of this public resource will rely on the generosity of the institutions that use the repository most. | proteome, storage, proteomics, distributed, server, mass spectrometry, protein, peptide, file sharing, security |
is listed by: Biositemaps has parent organization: University of Michigan; Ann Arbor; USA has parent organization: Proteome Commons |
NCI ; Clinical Proteomics Technologies for Cancer ; NCRR P41-RR018627 |
PMID:21063945 PMID:20356086 |
Open unspecified license (Apache v2); registration required . See Terms of Use, Https://proteomecommons.org/terms.jsp | nif-0000-33195 | http://tranche.proteomecommons.org | SCR_003441 | Tranche Project | 2026-02-14 02:00:33 | 8 | ||||
|
metagen Resource Report Resource Website 10+ mentions |
metagen (RRID:SCR_003443) | metagen | software resource | Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:17605724 | Free, Available for download, Freely available | OMICS_00238, biotools:metagen | https://www.rdocumentation.org/packages/meta/versions/4.9-6/topics/metagen | SCR_003443 | 2026-02-14 02:00:27 | 18 | ||||||
|
Innovative Medicines Initiative Resource Report Resource Website 100+ mentions |
Innovative Medicines Initiative (RRID:SCR_003754) | IMI | organization | Initiative to improve health by speeding up the development of, and patient access to, innovative medicines, particularly in areas where there is an unmet medical or social need. It does this by initiating and managing consortia composed of the key players involved in healthcare research, including universities, the pharmaceutical and other industries, small and medium-sized enterprises (SMEs), patient organizations, and medicines regulators. IMI is a public-private partnership between the European Union and the European pharmaceutical industry, represented by the European Federation of Pharmaceutical Industries and Associations (EFPIA), with a timeframe separated into two phases (2008-2013, 2014-2024) that are each defined by unique research agendas. The first phase (2008 2013) had four pillars that defined the focus of its research agenda: * Predicting safety: evaluating the safety of a compound during the pre-clinical phase of the development process and the later phases in clinical development. * Predicting efficacy: improving the ability to predict how a drug will interact in humans and how it may produce a change in function. * Knowledge management: utilization of information and data for predicting safety and efficacy. * Education and training: closing existing training gaps in the drug development process. Some of the consortia managed under IMI focused on specific health issues while others focused on broader challenges in drug development. Additionally, IMI launched a number of education and training projects during its first phases. The goal of the second phase (IMI2, 2014-2024) is to develop next generation vaccines and drugs. The focus is on delivering the right prevention and treatment for the right patient at the right time. There is a strong focus on the development of new medicines with an emphasis on tools and methods that accelerate patient access to new medicines. IMI2's agenda can be defined by four axes of research: * target validation and biomarker research (efficacy and safety) * adoption of innovative clinical trial paradigms * innovative medicines * patient-tailored adherence programs As part of its distinct goals, IMI2 aims to deliver: * 30% better success rate in clinical trials of priority medicines identified by the WHO; clinical proof of concept in immunological, respiratory, neurological and neurodegenerative diseases in five years; * new and approved diagnostic markers for four of these diseases and at least two new medicines which could either be new antibiotics or new therapies for Alzheimer's disease. | drug development, drug, tool development, biomarker, data sharing, target validation, safety, efficacy, clinical trial, medicine, adherence program, vaccine, consortium, diagnostic marker, oncology, drug discovery |
is listed by: Consortia-pedia is related to: AddNeuroMed is related to: European Federation of Pharmaceutical Industries and Associations has parent organization: European Union has parent organization: European Federation of Pharmaceutical Industries and Associations is parent organization of: AddNeuroMed |
European Union FP7 ; Horizon 2020 ; EFPIA ; Other life science industries or organizations |
Wikidata: Q1664196, nlx_157984, grid.454814.8, ISNI: 0000 0004 0577 0821 | https://ror.org/019af4n30 | SCR_003754 | 2026-02-14 02:00:52 | 275 | |||||||
|
Global Health Innovative Technology Fund Resource Report Resource Website 10+ mentions |
Global Health Innovative Technology Fund (RRID:SCR_003753) | GHIT Fund, GHIT | institution | A consortium that focuses their efforts on discovering and developing new pharmaceutical drugs, vaccines (both preventive and therapeutic) and diagnostics against the infectious diseases that are prevalent in developing countries. The initial targets are those disorders designated by WHO as neglected tropical diseases prevalent in developing nations. The consortium aims to facilitate international partnerships that enable Japanese technology, innovations, and insights to play a more direct role in improving global health. Another goal of GHIT is to develop a new drug-discovery screening platform to assist the screening of compound libraries housed within Japanese companies and academic institutions. The vision is to have Japanese research organizations donate compounds, with the Fund reimbursing screening costs and leveraging screening programs of existing product-development partners. | global health, health, drug development, biomarker, consortium, drug, vaccine, diagnostics, healthcare, developing country, disease | is listed by: Consortia-pedia | Government of Japan ; Bill and Melinda Gates Foundation ; Pharmaceutical industry |
grid.475132.6, nlx_157983 | https://ror.org/02yfqyv95 | SCR_003753 | 2026-02-14 02:00:35 | 16 | |||||||
|
Coca-Cola Company Resource Report Resource Website 1+ mentions |
Coca-Cola Company (RRID:SCR_003749) | Coca-Cola, KO | commercial organization | An American multinational beverage corporation and manufacturer, retailer and marketer of nonalcoholic beverage concentrates and syrups, which is headquartered in Atlanta, Georgia. (Wikipedia) It is the world's largest beverage company, refreshing consumers with more than 500 sparkling and still brands. | beverage | Crossref funder ID: 100004367, ISNI: 0000 0004 0504 2170, grid.451378.c, Wikidata: Q3295867, nlx_158091 | https://ror.org/00yc8qw13 | SCR_003749 | KO, The Coca-Cola Company, Coca-Cola | 2026-02-14 02:00:35 | 2 | ||||||||
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Seven Hills Bioreagents Resource Report Resource Website 1+ mentions |
Seven Hills Bioreagents (RRID:SCR_003748) | commercial organization | An Antibody supplier | nlx_152458 | SCR_003748 | 2026-02-14 02:00:51 | 3 | ||||||||||||
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RevMan Resource Report Resource Website 10000+ mentions |
RevMan (RRID:SCR_003581) | RevMan | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00244 | SCR_003581 | Review Manager | 2026-02-14 02:00:29 | 12961 | ||||||||
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Torrey Pines Biolabs Resource Report Resource Website 100+ mentions |
Torrey Pines Biolabs (RRID:SCR_003580) | commercial organization | An Antibody supplier | nlx_152481 | SCR_003580 | Torrey Pines Biolabs Inc., Torrey Pines Biolabs Inc | 2026-02-14 02:00:52 | 376 |
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