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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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ChIPpeakAnno Resource Report Resource Website 100+ mentions |
ChIPpeakAnno (RRID:SCR_012828) | ChIPpeakAnno | software resource | Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00804 | SCR_012828 | 2026-09-12 12:57:53 | 480 | ||||||||||
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MitoBreak Resource Report Resource Website 10+ mentions |
MitoBreak (RRID:SCR_012949) | MitoBreak | data or information resource, data repository, database, service resource, storage service resource | Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements. | mitochondrial dna rearrangement, mitochondrial dna, deletion, duplication, linear, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24170808 | Free, The community can contribute to this resource | biotools:mitobreak, OMICS_01640 | https://bio.tools/mitobreak | SCR_012949 | 2026-09-12 12:57:56 | 11 | ||||||
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NGSEP Resource Report Resource Website 50+ mentions |
NGSEP (RRID:SCR_012827) | NGSEP | data analysis software, data processing software, software application, software resource | Software whose main functionality is the variants detector, which allows to make simultaneous discovery of SNVs, small indels, and CNVs.Accurate variant calling across species and sequencing protocols.Used for analysis of DNA high throughput sequencing data. | matlab, variants detector, SNVs discovery, CNVs discovery, variant calling, species, sequencing protocols, bio.tools | is listed by: bio.tools | PMID:31099384 | Free, Available for download, Freely available | OMICS_00067, biotools:NGSEP | https://bio.tools/NGSEP | SCR_012827 | NGSEP3, Next Generation Sequencing Eclipse Plugin, Next Generation Sequencing Experience Platform | 2026-09-12 12:57:53 | 75 | |||||
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inSilicoMerging Resource Report Resource Website 10+ mentions |
inSilicoMerging (RRID:SCR_012829) | inSilicoMerging | software resource | Collection of techniques to remove inter-study bias when combining gene expression data originating from different studies. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00859 | SCR_012829 | 2026-09-12 12:57:53 | 41 | ||||||||||
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snapCGH Resource Report Resource Website 1+ mentions |
snapCGH (RRID:SCR_012947) | snapCGH | software resource | Software providing methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00734 | SCR_012947 | 2026-09-12 12:57:56 | 5 | ||||||||||
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ArrayTrack Resource Report Resource Website 50+ mentions |
ArrayTrack (RRID:SCR_012839) | ArrayTrack | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. |
uses: Gene Ontology For Functional Analysis (GOFFA) is listed by: OMICtools has parent organization: U.S. Food and Drug Administration |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00851 | SCR_012839 | 2026-09-12 12:57:53 | 66 | |||||||||
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Canadian Institutes of Health Research Resource Report Resource Website 100+ mentions |
Canadian Institutes of Health Research (RRID:SCR_012838) | CIHR | institution | The Canadian Institutes of Health Research (CIHR) is the Government of Canada''s agency responsible for funding health research in Canada. CIHR was created in 2000 under the authority of the CIHR Act and reports to Parliament through the Minister of Health. CIHR''s budget for 2008-09 is $928.6 million, of which $132 million is allocated to administering the Networks of Centres of Excellence and Canada Research Chair programs. CIHR was created to transform health research in Canada by: * funding more research on targeted priority areas; * building research capacity in under-developed areas such as population health and health services research; * training the next generation of health researchers; and * focusing on knowledge translation, so that the results of research are transformed into policies, practices, procedures, products and services. CIHR consists of 13 virtual institutes, a structure that is unique in the world. These innovative institutes bring together all partners in the research process - the people who fund research, those who carry it out and those who use its results - to share ideas and focus on what Canadians need: good health and the means to prevent disease and fight it when it happens. Each institute supports a broad spectrum of research in its topic areas and, in consultation with its stakeholders, sets priorities for research in those areas. |
is related to: Structural Genomics Consortium is parent organization of: Institute of Neurosciences Mental Health and Addiction is parent organization of: Institute of Aging - CIHR is parent organization of: International Initiative for Traumatic Brain Injury Research |
grid.248883.d, ISNI: 000000010789659X, Crossref funder ID: 501100000024, Wikidata: Q5030193, nlx_45689 | https://ror.org/01gavpb45 | SCR_012838 | Instituts de recherche en sante du Canada, IRSC | 2026-09-12 12:57:53 | 486 | ||||||||
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NCCN Resource Report Resource Website 500+ mentions |
NCCN (RRID:SCR_012959) | data or information resource, disease-related portal, portal, topical portal | A not-for-profit alliance of 23 cancer centers devoted to patient care, research, and education, is dedicated to improving the quality, effectiveness, and efficiency of cancer care so that patients can live better lives. Through the leadership and expertise of clinical professionals at NCCN Member Institutions, NCCN develops resources that present valuable information to the numerous stakeholders in the health care delivery system. As the arbiter of cancer care, NCCN promotes the importance of continuous quality improvement and recognizes the significance of creating clinical practice guidelines appropriate for use by patients, clinicians, and other health care decision-makers. | nlx_156880 | SCR_012959 | National comprehensive cancer network | 2026-09-12 12:57:56 | 691 | |||||||||||
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minfi Resource Report Resource Website 100+ mentions |
minfi (RRID:SCR_012830) | minfi | data analysis software, data processing software, data visualization software, software application, software resource | Software tools for analyzing and visualizing Illumina''s 450k array data. | Illumina, array data, Analyze Illumina Infinium DNA methylation arrays, DNA methylation array, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SWAN has parent organization: Bioconductor |
PMID:28035024 | Free, Available for download, Freely available | biotools:minfi, OMICS_00799, BioTools:minfi | https://bio.tools/minfi, https://bio.tools/minfi, https://bio.tools/minfi | SCR_012830 | 2026-09-12 12:57:53 | 417 | ||||||
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miRNApath Resource Report Resource Website 1+ mentions |
miRNApath (RRID:SCR_012833) | miRNApath | software resource | Software package that provides pathway enrichment techniques for miRNA expression data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00787 | SCR_012833 | 2026-09-12 12:57:53 | 5 | ||||||||||
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RepeatMasker Resource Report Resource Website 10000+ mentions |
RepeatMasker (RRID:SCR_012954) | software resource | Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ). |
uses: Repbase uses: RMBlast is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
DOI:10.1007/978-1-61779-603-6_2 | nlx_156840, OMICS_09436 | https://sources.debian.org/src/repeatmasker/ | SCR_012954 | repeatmasker.org | 2026-09-12 12:57:56 | 10730 | ||||||||
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National Environmental Public Health Tracking Program Resource Report Resource Website 10+ mentions |
National Environmental Public Health Tracking Program (RRID:SCR_012832) | data or information resource, portal, topical portal | The goal of environmental public health tracking is to protect communities by providing information to federal, state, and local agencies. These agencies, in turn, will use this information to plan, apply, and evaluate public health actions to prevent and control environmentally related diseases. Environmental public health tracking is the ongoing collection, integration, analysis, and interpretation of data about the following factors: :- Environmental hazards :- Exposure to environmental hazards :- Health effects potentially related to exposure to environmental hazards CDC''s goal is to develop a tracking system that integrates data about environmental hazards and exposures with data about diseases that are possibly linked to the environment. This system will allow federal, state, and local agencies, and others to do the following: :- monitor and distribute information about environmental hazards and disease trends :- advance research on possible linkages between environmental hazards and disease :- develop, implement, and evaluate regulatory and public health actions to prevent or control environment-related diseases. Planning for an environmental public health tracking network is an important priority for CDC because of the opportunity it provides to address some of the most challenging problems facing local, state, and national public health leaders. From the outset, this activity has involved substantial collaboration between CDC and its public health and environmental partners (e.g., see the memorandum of understanding between HHS/CDC and the Environmental Protection Agency). Sponsors: This resource is supported by the Center for Disease Control and Prevention. Keywords: Environment, Public, Health, Disease, Analysis, Integration, Data, Hazard, Health, Prevention, | has parent organization: Centers for Disease Control and Prevention | nif-0000-30243 | SCR_012832 | NEPHT Program | 2026-09-12 12:57:53 | 11 | ||||||||||
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affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | data analysis software, data processing software, software application, software resource | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-09-12 12:57:53 | 3073 | ||||
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NINDS Parkinsons Disease Research Web Resource Report Resource Website |
NINDS Parkinsons Disease Research Web (RRID:SCR_012834) | data or information resource, disease-related portal, portal, research forum portal, topical portal | This NINDS website is designed to facilitate research efforts on Parkinsons disease, as well as to provide researchers, patients and caregivers with related information and resources. Because the interests of the research and patient communities are overlapping yet distinct, the site contains separate web pages directed toward these two communities. For example, regarding funding for PD research, researchers will find information on relevant research funding opportunities, and people with PD can access information on currently funded NINDS and NIH projects. As part of their mission to decrease the burden of neurological disease, and building upon a strong foundation of research discovery, the NINDS is committed to the rapid translation of basic research findings into clinical practice. The NINDS supports a broad spectrum of basic, translational and clinical research on Parkinsons disease (PD), a chronic, progressive movement disorder that affects the lives of at least one million patients across the United States. The average onset of characteristic motor symptoms, which are initially subtle and impact purposeful movement, occurs in the sixth decade. People with PD also experience significant non-motor symptoms including changes in cognition and mood, sleep disturbances, and autonomic dysfunction. Currently available pharmacological and surgical treatments provide relief from some motor symptoms, but do not halt the ultimate progression of the disease. Although significant research advances have been made, including the recent identification of possible environmental and genetic risk factors, a clear cause and a definitive cure for PD have remained elusive. Through a constellation of funding mechanisms, representing over 86 million in fiscal year 2008, the NINDS promotes the advancement of research directed to the understanding, treatment and eventual cure of PD. Sponsors: This resource is supported by the National Institute of Neurological Disorders and Stroke. Keywords: Stroke, Neurological, Disorder, Research, Disease, Researcher, Clinical, Parkinson''s Disease, PD, Chronic, Treatment, Cure, Motor, Genetic, Environmental, | nif-0000-37629 | SCR_012834 | Parkinsons Disease Research Web | 2026-09-12 12:57:53 | 0 | |||||||||||
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sva package Resource Report Resource Website 100+ mentions |
sva package (RRID:SCR_012836) | sva package | software resource | Contains functions for removing batch effects and other unwanted variation in high-throughput experiment. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00861 | SCR_012836 | Surrogate Variable Analysis | 2026-09-12 12:57:53 | 100 | |||||||||
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USDA National Institute of Food and Agriculture Resource Report Resource Website 10+ mentions |
USDA National Institute of Food and Agriculture (RRID:SCR_012886) | NIFA, CSREES | government granting agency | is parent organization of: Current Research Information System | SCR_012886 | U.S. Department of Agriculture Cooperative State Research Education and Extension Service, U.S. Department of Agriculture National Institute of Food and Agriculture, USDA Cooperative State Research Education and Extension Service, National Institute of Food and Agriculture, United States Department of Agriculture National Institute of Food and Agriculture, Cooperative State Research Education and Extension Service, United States Department of Agriculture Cooperative State Research Education and Extension Service | 2026-09-12 12:57:54 | 26 | |||||||||||
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National Institute of General Medical Sciences Resource Report Resource Website 500+ mentions |
National Institute of General Medical Sciences (RRID:SCR_012887) | NIGMS | institution | NIGMS supports basic biomedical research that is not targeted to specific diseases. NIGMS funds studies on genes, proteins, and cells, as well as on fundamental processes like communication within and between cells, how our bodies use energy, and how we respond to medicines. The results of this research increase our understanding of life and lay the foundation for advances in disease diagnosis, treatment, and prevention. NIGMS also supports research training programs that produce the next generation of biomedical scientists, and it has special programs to encourage underrepresented minorities to pursue biomedical research careers. The National Institute of General Medical Sciences (NIGMS) primarily supports research that lays the foundation for advances in disease diagnosis, treatment, and prevention. The Institute's research training programs help provide the next generation of scientists. Each year, NIGMS-supported scientists make many advances in understanding fundamental life processes. In the course of answering basic research questions, these investigators increase our knowledge about the mechanisms and pathways involved in certain diseases. Institute grantees also develop important new tools and techniques, some of which have medical applications. In recognition of the significance of their work, a number of NIGMS grantees have received the Nobel Prize and other high scientific honors. At any given time, NIGMS supports approximately 4,700 research grants—approximately 11 percent of the grants funded by NIH as a whole. NIGMS also supports approximately 26 percent of the trainees who receive assistance from NIH. NIGMS also supports approximately 25% of the trainees who receive assistance from NIH. The Institute places great emphasis on supporting investigator-initiated research grants. It funds a limited number of research center grants in selected fields, including structural genomics, trauma and burn research, and systems biology. In addition, NIGMS supports several important scientific resources, including the NIGMS Human Genetic Cell Repository and the Protein Data Bank. |
has parent organization: NIH Blueprint for Neuroscience Research has parent organization: National Institutes of Health is parent organization of: Generic Model Organism Database Project is parent organization of: National Institute of General Medical Sciences: Research Funding is parent organization of: National Institute of General Medical Sciences Image Gallery is parent organization of: NIGMS - YouTube is parent organization of: NIGMS Multimedia is parent organization of: NIGMS Computing Life is parent organization of: ChemHealthWeb is parent organization of: NIGMS Inside Life Science is parent organization of: MeRNA |
grid.280785.0, ISNI: 0000 0004 0533 7286, Wikidata: Q6973666, nlx_inv_1005108, Crossref funder ID: 100000057 | https://ror.org/04q48ey07 | SCR_012887 | 2026-09-12 12:57:54 | 564 | |||||||||
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Newcastle University; Newcastle upon Tyne; United Kingdom Resource Report Resource Website 1+ mentions |
Newcastle University; Newcastle upon Tyne; United Kingdom (RRID:SCR_012923) | Newcastle University | university | UK public research university based in Newcastle upon Tyne, North East England with overseas campuses in Singapore and Malaysia. The university is a red brick university and a member of the Russell Group, an association of research-intensive UK universities. |
is parent organization of: Code Analysis Repository and Modelling for e-Neuroscience is parent organization of: eDoctoring is parent organization of: SINOMO is parent organization of: DONE: Detection of Outlier NEurons is parent organization of: HUDSEN is parent organization of: Human Developmental Biology Resource is parent organization of: Newcastle University Bioinformatics Support Unit is parent organization of: Newcastle University Labs and Facilities is parent organization of: HUDSEN Electronic Atlas of the Developing Human Brain is parent organization of: JEPETTO is parent organization of: Newcastle Brain Tissue Resource is parent organization of: Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) is parent organization of: Newcastle University Bioimaging Unit Core Facility |
grid.1006.7, nlx_51333, Crossref funder ID:501100008406, Wikidata:Q837164, ISNI:0000 0001 0462 7212 | https://ror.org/01kj2bm70 | SCR_012923 | Newcastle University; Newcastle; United Kingdom, Newcastle University; Newcastle-upon-Tyne; United Kingdom | 2026-09-12 12:57:55 | 4 | ||||||||
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NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases Resource Report Resource Website 100+ mentions |
NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases (RRID:SCR_012895) | NIDDK | government granting agency | Center with mission to conduct and support medical research and research training and to disseminate science-based information on diabetes and other endocrine and metabolic diseases. The NIDDK supports a wide range of medical research through grants to universities and other medical research institutions across the country. | diabetes, metabolic disease, digestive, kidney, endocrine, medical research |
recommends: Cell Image Library (CIL) recommends: Biological General Repository for Interaction Datasets (BioGRID) recommends: NIDDK Central Repository recommends: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) recommends: Metabolomics Workbench recommends: PeptideAtlas recommends: Network Data Exchange (NDEx) recommends: Mouse Genome Informatics (MGI) recommends: Zebrafish Information Network (ZFIN) recommends: FlyBase recommends: Database of Interacting Proteins (DIP) recommends: WormBase recommends: PhysioNet recommends: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) recommends: UniProt recommends: dbSNP recommends: DNA DataBank of Japan (DDBJ) recommends: European Nucleotide Archive (ENA) recommends: dbVar recommends: ClinicalTrials.gov recommends: European Variation Archive (EVA) recommends: MGnify recommends: Analysis, Visualization, and Informatics Lab-space (AnVIL) recommends: GenBank recommends: Gene Expression Omnibus (GEO) recommends: miRBase recommends: Database of Genomic Variants Archive (DGVa) recommends: Crystallography Open Database (COD) recommends: Coherent X-Ray Imaging Data Bank (CXIDB) recommends: Biological Magnetic Resonance Data Bank (BMRB) recommends: Worldwide Protein Data Bank (wwPDB) recommends: EMDataResource.org recommends: NCBI Assembly Archive Viewer recommends: Cambridge Crystallographic Data Centre (CCDC) recommends: Inorganic Crystal Structure Database (ICSD) recommends: Structural Biology Grid recommends: ArrayExpress recommends: GenomeRNAi recommends: NCBI database of Genotypes and Phenotypes (dbGap) recommends: Protein Circular Dichroism Data Bank (PCDDB) recommends: Electron Microscopy Data Bank at PDBe (MSD-EBI) recommends: PDBe - Protein Data Bank in Europe recommends: PubChem BioAssay recommends: Japanese Genotype-phenotype Archive (JGA) recommends: ProteomeXchange recommends: IntAct recommends: European Genome phenome Archive recommends: MetaboLights recommends: PubChem Substance recommends: The Immunology Database and Analysis Portal (ImmPort) recommends: STRENDA recommends: Kinetic Models of Biological Systems (KiMoSys) recommends: FLOWRepository recommends: Mass spectrometry Interactive Virtual Environment (MassIVE) recommends: Global Proteome Machine Database (GPM DB) recommends: Cancer Imaging Archive (TCIA) recommends: German Neuroinformatics Node (G-Node) recommends: 1000 Functional Connectomes Project recommends: ChEMBL recommends: Image Data Resource (IDR) recommends: SICAS Medical Image Repository recommends: ZENODO recommends: Dataverse Network Project recommends: NeuroMorpho.Org recommends: Mendeley Data recommends: NIMH Data Archive recommends: NIH Figshare Archive recommends: FigShare recommends: National Addiction and HIV Data Archive Program (NAHDAP) recommends: Dryad Digital Repository recommends: Open Science Framework recommends: OpenNeuro recommends: SPARC Portal lists: Mutant Mouse Resource and Research Center lists: NIDDK Research Resources is affiliated with: Cystic Fibrosis Research and Translation Centers is affiliated with: Nutrition and Obesity Research Centers is affiliated with: O'Brien Urology Centers is affiliated with: Hematology Centers is affiliated with: Polycystic Kidney Disease Research and Translation Centers is affiliated with: O'Brien Kidney Centers is affiliated with: Diabetes Research Centers is affiliated with: Digestive Disease Centers is affiliated with: Centers for Diabetes Translation Research is affiliated with: Pediatric Centers of Excellence in Nephrology is affiliated with: Focal Segmental Glomerulosclerosis in Children and Young Adults Interventional Study is related to: Bridging Interventional Development Gaps is related to: Polycystic Kidney Disease Research Resource Consortium has parent organization: National Institutes of Health is parent organization of: MTOPS Prostate Samples Analysis Consortium is parent organization of: Symptom Score for Benign Prostatic Hyperplasia is parent organization of: Type 1 Diabetes - Rapid Access to Intervention Development is parent organization of: National Diabetes Education Program is parent organization of: Family Investigation of Nephropathy of Diabetes is parent organization of: Frequent Hemodialysis Network Daily Trial is parent organization of: HemBase is parent organization of: NIDDK- National Institute of Diabetes and Digestive and Kidney Diseases Obesity Resources is parent organization of: dkCOIN is parent organization of: National Kidney Disease Education Program is parent organization of: Network of Minority Health Research Investigators is parent organization of: National Endocrine and Metabolic Diseases Information Service is parent organization of: National Diabetes Information Clearinghouse is parent organization of: National Digestive Diseases Information Clearinghouse is parent organization of: National Hematologic Diseases Information Service is parent organization of: National Kidney and Urologic Diseases Information Clearinghouse is parent organization of: Type 1 Diabetes Preclinical Testing Program is parent organization of: Frequent Hemodialysis Network Nocturnal Trial is parent organization of: Boston Area Community Health Survey is parent organization of: Minimally Invasive Surgical Therapies Treatment Consortium for Benign Prostatic Hyperplasia is parent organization of: Focal Segmental Glomerulosclerosis in Children and Young Adults Interventional Study |
Type 1 diabetes, Type 2 diabetes, Diabetes, Digestive disease, Kidney disease, Endocrine disease, Obesity, Blood disease, Liver disease, Urologic disease | nlx_inv_1005102 | SCR_012895 | National Institute of Diabetes and Digestive and Kidney Diseases | 2026-09-12 12:57:55 | 156 | |||||||
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BRAINSTracer Resource Report Resource Website 1+ mentions |
BRAINSTracer (RRID:SCR_012894) | BRAINSTracer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3, and integrates the Slicer3 theme. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: BRAINSTools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155705 | http://www.nitrc.org/projects/brainstracer | SCR_012894 | 2026-09-12 12:57:55 | 5 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
