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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MiRaGE Resource Report Resource Website 10+ mentions |
MiRaGE (RRID:SCR_012738) | MiRaGE | software resource | Software package that contains functions for inference of target gene regulation by miRNA, based on only target gene expression profile. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00785 | SCR_012738 | 2026-08-01 12:04:40 | 29 | ||||||||||
|
Samuel Roberts Noble Foundation Resource Report Resource Website 1+ mentions |
Samuel Roberts Noble Foundation (RRID:SCR_012794) | Noble Foundation | institution | The Samuel Roberts Noble Foundation is an independent, nonprofit institute headquartered in Ardmore, Okla. Founded in 1945, the Noble Foundation conducts direct operations, including assisting farmers and ranchers, and conducting plant science research and agricultural programs, to enhance agricultural productivity regionally, nationally and internationally. Employing more than 360 persons, the Noble Foundation conducts its operations through the activities of three operating divisions: * Agricultural Division: Serving a 47-county area within a 100-mile radius of the Noble Foundation''s headquarters in Ardmore, Okla., the Agricultural Division assists more than 1,700 regional farmers and ranchers in achieving their individual financial, production, stewardship and quality-of life goals. * Plant Biology Division: The Plant Biology Division conducts basic biochemical, genetic and genomic plant research for the purpose of improving crop productivity and value, and enhancing animal and human health. * Forage Improvement Division: The Forage Improvement Division translates basic plant science research into tangible plant varieties. Within the institution, the Forage Improvement Division serves as a link between the discoveries in the laboratory and the field, where such discoveries are intended to enhance agricultural outcomes in Oklahoma and around the world. The coordinated efforts of these operating divisions enable the Noble Foundation agricultural specialists and scientists to move science and innovation from the laboratory to the field, giving life to discovery and improving agriculture in Oklahoma, in the United States and around the world. |
is parent organization of: MedicCyc is parent organization of: LegumeIP is parent organization of: PlantTFcat is parent organization of: psRNATarget |
ISNI: 0000 0004 0370 5663, nlx_151456, grid.419447.b, Crossref funder ID: 100000944 | https://ror.org/02zta5505 | SCR_012794 | Noble Foundation | 2026-08-01 12:04:39 | 5 | ||||||||
|
Chinese Academy of Sciences; Beijing; China Resource Report Resource Website 10+ mentions |
Chinese Academy of Sciences; Beijing; China (RRID:SCR_012797) | CAS | university | Public university for graduate education, under the direct leadership of the Chinese Academy of Sciences. |
is parent organization of: pFind Studio: pLink is parent organization of: Cascleave is parent organization of: rSNPBase is parent organization of: pNovo+ is parent organization of: pLabel is parent organization of: pBuild is parent organization of: Human Potential Tumor Associated Antigen database is parent organization of: pFind is parent organization of: Linked Neuron Data is parent organization of: QC-Chain is parent organization of: Network Ontology Analysis is parent organization of: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit is parent organization of: Human Protein-Protein Interaction Mining Tool is parent organization of: Database of Domain Interactions and Bindings is parent organization of: Group Information Guided ICA is parent organization of: Groupwise Image Registration Toolbox is parent organization of: Local Label Learning Segmentation is parent organization of: Shanghai Institutes for Biological Sciences; Shanghai; China is parent organization of: GPU-Meta-Storms is parent organization of: EPGD is parent organization of: MethyCancer is parent organization of: inGAP is parent organization of: SysZNF - C2H2 Zinc Finger genes is parent organization of: NONCODE is parent organization of: Systematic Platform for Identifying Mutated Proteins (SysPIMP) is parent organization of: IVDB - Influenza Virus Database is parent organization of: Brainnetome fMRI toolkit is parent organization of: Brainnetome Atlas Viewer is parent organization of: Automatic Tractography-based Parcellation Pipeline |
grid.9227.e, Wikidata: Q530471, ISNI: 119573309, Crossref funder ID: 501100002367, nlx_47801 | https://ror.org/034t30j35 | SCR_012797 | Chinese Academy of Sciences | 2026-08-01 12:04:51 | 30 | ||||||||
|
U.S. Department of Defense Resource Report Resource Website 10+ mentions |
U.S. Department of Defense (RRID:SCR_012712) | DOD | institution | Executive branch department of the federal government charged with coordinating and supervising all agencies and functions of the government directly related to national security and the United States Armed Forces. | Government granting agency |
is parent organization of: Defense Advanced Research Projects Agency is parent organization of: Office of Naval Research is parent organization of: Defense and Veterans Brain Injury Center is parent organization of: Defense Centers of Excellence for Psychological Health and Traumatic Brain Injury is parent organization of: Congressionally Directed Medical Research Program is parent organization of: BHSAI; Maryland; USA |
ISNI: 0000 0004 0478 6223, grid.420391.d, nlx_143670, Crossref funder ID: 100000005, Wikidata: Q11209 | https://ror.org/0447fe631 | SCR_012712 | Department of Defense, United States Department of Defense, US Department of Defense | 2026-08-01 12:04:38 | 41 | |||||||
|
GNU.org Resource Report Resource Website 100+ mentions |
GNU.org (RRID:SCR_012764) | software resource | Unix-like operating system that is free software. GNU (more precisely, GNU/Linux systems) are entirely free software. The GNU Project was launched in 1984 to develop the GNU system. A Unix-like operating system is a software collection of applications, libraries, and developer tools, plus a program to allocate resources and talk to the hardware, known as a kernel. The Hurd, GNU''s own kernel, is some way from being ready for daily use. Thus, GNU is typically used today with a kernel called Linux. This combination is the GNU/Linux operating system. GNU/Linux is used by millions, though many call it Linux by mistake. | nlx_156924 | SCR_012764 | 2026-08-01 12:04:39 | 173 | ||||||||||||
|
MotifLab Resource Report Resource Website 1+ mentions |
MotifLab (RRID:SCR_012649) | MotifLab | software resource | Software for a general workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. |
is listed by: OMICtools has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
Research Council of Norway | PMID:23323883 | Acknowledgement requested, Free, Public | OMICS_00486 | SCR_012649 | 2026-08-01 12:04:38 | 2 | |||||||
|
tRanslatome Resource Report Resource Website 1+ mentions |
tRanslatome (RRID:SCR_012810) | tRanslatome | software resource | Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression, using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24222209 | Free | OMICS_01316 | SCR_012810 | tRanslatome - Comparison between multiple levels of gene expression | 2026-08-01 12:04:40 | 2 | |||||||
|
Krona Resource Report Resource Website 50+ mentions |
Krona (RRID:SCR_012785) | Krona | software resource | Software that allows hierarchical data to be explored with zoomable pie charts. | bio.tools |
is listed by: bio.tools has parent organization: SourceForge |
PMID:21961884 | OMICS_01498, biotools:krona | https://bio.tools/krona | SCR_012785 | Krona - Hierarchical data browser | 2026-08-01 12:04:41 | 89 | ||||||
|
U.S. Social Security Administration Resource Report Resource Website 1+ mentions |
U.S. Social Security Administration (RRID:SCR_012905) | SSA | institution | Independent agency of the U.S. federal government that administers Social Security, a social insurance program consisting of retirement, disability, and survivor benefits. | Government granting agency | is parent organization of: New Beneficiary Data System | Crossref funder ID: 100005225, ISNI: 0000 0001 0726 0196, nlx_151831, grid.453277.0, Wikidata: Q2824618 | https://ror.org/04b7xxn32 | SCR_012905 | Social Security Administration, Social Security Administration (SSA) | 2026-08-01 12:04:42 | 6 | |||||||
|
BEDOPS Resource Report Resource Website 100+ mentions |
BEDOPS (RRID:SCR_012865) | BEDOPS | software resource | A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets. |
is listed by: OMICtools is listed by: Debian |
PMID:22576172 DOI:10.1093/bioinformatics/bts277 |
GNU General Public License, v3 | OMICS_00949 | https://sources.debian.org/src/bedops/ | SCR_012865 | BEDOPS: high-performance genomic feature operations | 2026-08-01 12:04:42 | 220 | ||||||
|
EYE-EEG (combined eye-tracking & EEG) Resource Report Resource Website 10+ mentions |
EYE-EEG (combined eye-tracking & EEG) (RRID:SCR_012903) | EYE-EEG | software resource | A plugin for the open-source MATLAB toolbox EEGLAB developed with the goal to facilitate integrated analyses of electrophysiological and oculomotor data. The plugin parses, imports, and synchronizes simultaneously recorded eye tracking data and adds it as extra channels to the EEG. Saccades and fixations can be imported from the eye tracking raw data or detected with an adaptive velocity-based algorithm. Eye movements are then added as new time-locking events to EEGLAB's event structure, allowing easy saccade- and fixation-related EEG analysis (e.g., fixation-related potentials, FRPs). Alternatively, EEG data can be aligned to stimulus onsets and analyzed according to oculomotor behavior (e.g. pupil size, microsaccades) in a given trial. Saccade-related ICA components can be objectively identified based on their covariance with the electrically independent eye tracker. All functions can be accessed via EEGLAB's GUI or called from the command line. | eeg, meg, electrocorticography, matlab, os independent, eye, electrophysiology, oculomotor, eye tracking device |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: EEGLAB has parent organization: Humboldt University of Berlin; Berlin; Germany |
DFG | PMID:21744985 | GNU General Public License | nlx_155755 | http://www.nitrc.org/projects/eye-eeg | SCR_012903 | EYE-EEG: Eye tracking & EEG | 2026-08-01 12:04:53 | 13 | ||||
|
GENSCAN Resource Report Resource Website 100+ mentions |
GENSCAN (RRID:SCR_012902) | service resource | Resource out of service. Documented on February 24,2021. | has parent organization: German Cancer Research Center | Resource out of service. Documented on February 24,2021. | nif-0000-30609 | SCR_012902 | GENSCAN | 2026-08-01 12:04:53 | 192 | |||||||||
|
Flash Gviewer Resource Report Resource Website 1+ mentions |
Flash Gviewer (RRID:SCR_012870) | Flash GViewer | software resource | Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool | visualization, chromosome, video, gene, qtl, genome, navitgation, phenotype, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Medical College of Wisconsin; Wisconsin; USA |
Free for academic use | nlx_149333 | http://gmod.org/flashgviewer | SCR_012870 | 2026-08-01 12:04:42 | 2 | |||||||
|
featureCounts Resource Report Resource Website 10000+ mentions |
featureCounts (RRID:SCR_012919) | featureCounts | software resource | A read summarization program, which counts mapped reads for the genomic features such as genes and exons. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is required by: SL-quant |
PMID:24227677 | biotools:featurecounts, OMICS_01160 | https://bio.tools/featurecounts | SCR_012919 | featureCounts: a universal read summarization program | 2026-08-01 12:04:53 | 12197 | ||||||
|
Netherlands Bioinformatics Centre Resource Report Resource Website 1+ mentions |
Netherlands Bioinformatics Centre (RRID:SCR_012879) | NBIC | institution | A collaborative institute of the bioinformatics groups in the Netherlands that perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. They aim to build and maintain a strong bioinformatics and e-bioscience community that meets the (growing) demand for bioinformatics expertise, infrastructure and personnel in the Dutch life sciences field and provides a stimulating force for advanced research in biology. The NBIC grants aim to support the NBIC projects and (the visibility of) the NBIC community. Therefore, only people working in NBIC partner organizations can apply for sponsoring by NBIC. Positions for postdocs and others are available and there is a yearly conference. |
is related to: Open PHACTS is parent organization of: CoPub is parent organization of: WISECONDOR is parent organization of: PASSion is parent organization of: Concept Web Alliance is parent organization of: NARWHAL |
nif-0000-03485, grid.450192.b, Wikidata: Q6999142 | https://ror.org/01r0k6965 | SCR_012879 | Stichting Netherlands Bioinformatics Center, Stichting Netherlands Bioinformatics Centre, Netherlands Bioinformatics Center | 2026-08-01 12:04:52 | 2 | ||||||||
|
United States Department of Energy Resource Report Resource Website 50+ mentions |
United States Department of Energy (RRID:SCR_012841) | DOE | institution | The mission of the Department of Energy is to ensure America''s security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. Goal 1: Transform our Energy Systems - Catalyze the timely, material, and efficient transformation of the nation''s energy system and secure U.S. leadership in clean energy technologies. Goal 2: The Science and Engineering Enterprise - Maintain a vibrant U.S. effort in science and engineering as a cornerstone of our economic prosperity, with clear leadership in strategic areas. Goal 3: Secure Our Nation - Enhance nuclear security through defense, nonproliferation, and environmental efforts. Goal 4: Management and Operational Excellence - Establish an operational and adaptable framework that combines the best wisdom of all Department stakeholders to maximize mission success. |
is parent organization of: Microbial Genomics Program is parent organization of: Argonne National Laboratory is parent organization of: Brookhaven National Laboratories; New York; USA is parent organization of: Human Genome Project Information |
nlx_86742, grid.85084.31, Wikidata: Q217810, ISNI: 123423717, Crossref funder ID: 100000015 | https://ror.org/01bj3aw27 | SCR_012841 | US Department of Energy, U.S. Department of Energy, Department of Energy, U.S. DOE, US DOE | 2026-08-01 12:04:40 | 63 | ||||||||
|
USAID Resource Report Resource Website 100+ mentions |
USAID (RRID:SCR_012846) | USAID | government granting agency | is parent organization of: DHS Program | SCR_012846 | U.S. Agency for International Development, US Agency for International Development, US AID, USAID from the American people | 2026-08-01 12:04:40 | 473 | |||||||||||
|
dmrFinder Resource Report Resource Website 10+ mentions |
dmrFinder (RRID:SCR_012853) | dmrFinder | software resource | Function for differentially methylated regions (DMR) detection that is a part of the charm package in R/Bioconductor. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00621 | SCR_012853 | 2026-08-01 12:04:42 | 27 | ||||||||||
|
Mauve Resource Report Resource Website 1000+ mentions |
Mauve (RRID:SCR_012852) | Mauve | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software as system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. | bio.tools |
is listed by: bio.tools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
DOI:10.1101/gr.2289704 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00940, biotools:mauve | https://bio.tools/mauve | http://gel.ahabs.wisc.edu/mauve/ | SCR_012852 | 2026-08-01 12:04:40 | 1569 | |||||
|
Django Resource Report Resource Website 500+ mentions |
Django (RRID:SCR_012855) | software resource | Django is a high-level Python Web framework that encourages rapid development and clean, pragmatic design. Developed four years ago by a fast-moving online-news operation, Django was designed to handle two challenges: the intensive deadlines of a newsroom and the stringent requirements of the experienced Web developers who wrote it. It lets you build high-performing, elegant Web applications quickly. Django focuses on automating as much as possible and adhering to the DRY principle. | nif-0000-30460 | SCR_012855 | Django | 2026-08-01 12:04:52 | 561 |
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