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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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National Institute on Deafness and Other Communication Disorders Resource Report Resource Website 50+ mentions |
National Institute on Deafness and Other Communication Disorders (RRID:SCR_012859) | NIDCD | institution | The National Institute on Deafness and Other Communication Disorders (NIDCD) is one of the Institutes that comprise the National Institutes of Health (NIH). Established in 1988, NIDCD is mandated to conduct and support biomedical and behavioral research and research training in the normal and disordered processes of hearing, balance, smell, taste, voice, speech, and language. The Institute also conducts and supports research and research training related to disease prevention and health promotion; addresses special biomedical and behavioral problems associated with people who have communication impairments or disorders; and supports efforts to create devices which substitute for lost and impaired sensory and communication function. It is estimated that more than 46 million people in the United States suffer some form of disordered communication. NIDCD has focused national attention on disorders of human communication and has contributed to advances in biomedical and behavioral research that will improve the lives of millions of individuals with communication disorders. NIDCD has made important contributions to the body of knowledge needed to help those who experience communication disorders and to advance research in all aspects of human communication. NIDCD accomplishes its mandate through the Division of Intramural Research, which conducts research in laboratories at the NIH, and the Extramural Research Program, a program of research grants, career development awards, individual and institutional research training awards, center grants, and contracts to public and private research institutions and organizations. As a whole, the Institute supports and conducts approximately 600 research projects. The Institute also conducts and supports research and research training in disease prevention and health promotion and the special biomedical and behavioral problems associated with people having communication impairments and disorders. NIDCD''s extramural grant portfolio demonstrates a balance of basic and clinical research. The intramural research program spans a variety of topics, including, but not limited to, the development of a vaccine against otitis media, the identification and characterization of genes responsible for hereditary hearing impairment, genes associated with neoplasms affecting human communication, and treatment of voice disorders. |
has parent organization: NIH Blueprint for Neuroscience Research has parent organization: National Institutes of Health |
nlx_inv_1005114, Crossref funder ID: 100000055, Wikidata: Q10843453, grid.214431.1, ISNI: 0000 0001 2226 8444 | https://ror.org/04mhx6838 | SCR_012859 | National Institute on Deafness Other Communication Disorders | 2026-08-01 12:04:52 | 75 | ||||||||
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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 | 2026-08-01 12:04:52 | 448 | ||||||||||
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MitoBreak Resource Report Resource Website 10+ mentions |
MitoBreak (RRID:SCR_012949) | MitoBreak | data or information resource, data repository, storage service resource, database, 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 | 2026-08-01 12:04:42 | 10 | ||||||
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NGSEP Resource Report Resource Website 50+ mentions |
NGSEP (RRID:SCR_012827) | NGSEP | data processing software, data analysis 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 | 2026-08-01 12:04:40 | 69 | |||||
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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 | 2026-08-01 12:04:40 | 37 | ||||||||||
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Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) Resource Report Resource Website 5000+ mentions |
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) | RCSB PDB | data or information resource, data repository, storage service resource, database, service resource | Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results. | 3-dimensional, annotation, molecule, nucleic acid, protein, visualization, sequence, function, macromolecule, ligand, model, dna, x-ray crystallography, ribosome, structure, oncogene, nucleic acids, molecular structure, cryomicroscopy, gold standard, FASEB list |
is used by: Structural Genomics Consortium is used by: Ligand Expo is used by: DARC - Database for Aligned Ribosomal Complexes is used by: FireDB is used by: Protein Data Bank Bind Database is used by: Protein Data Bank Site is used by: NIF Data Federation is used by: ChannelPedia is used by: MobiDB is used by: BALBES is used by: Structural Antibody Database is used by: BioLiP is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is affiliated with: EMDataResource.org is affiliated with: ConSurf Database is related to: pdb-data is related to: PDB2MultiGif is related to: GlyProt is related to: pdb-care is related to: pdb2linucs is related to: GlyVicinity is related to: GlyTorsion is related to: GlySeq is related to: AffinDB is related to: StatAlign is related to: Community Structure-Activity Resource is related to: Binding MOAD is related to: ConSurf Database is related to: glycosciences.de is related to: DOMINE: Database of Protein Interactions is related to: Jenalib: Jena Library of Biological Macromolecules is related to: SynSysNet is related to: EMDataResource.org is related to: PDBe - Protein Data Bank in Europe is related to: TFinDIT is related to: HOLLOW is related to: ccPDB - Compilation and Creation of datasets from PDB is related to: DOMMINO - Database Of MacroMolecular INteractiOns is related to: InterEvol database is related to: Polbase is related to: PoSSuM is related to: ProtChemSI is related to: RNA CoSSMos is related to: PDBsum is related to: Worldwide Protein Data Bank (wwPDB) is related to: canSAR is related to: CAPS Database is related to: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING is related to: Combinatorial Extension (CE) is related to: Metalloprotein Site Database is related to: PDBj - Protein Data Bank Japan is related to: Statistical Torsional Angles Potentials of NMR Refinement Database is related to: Metalloprotein Ligand Interaction Database is related to: CARP is related to: PDBTM is related to: RNA FRABASE - RNA FRAgments search engine and dataBASE is related to: AmiGO is related to: ConsensusPathDB is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: FlyMine is related to: NCBI Protein Database is related to: NCBI Nucleotide is related to: FunTree is related to: IndelFR - Indel Flanking Region Database is related to: NMR Restraints Grid is related to: Enzyme Structures Database is related to: Electron Microscopy Data Bank at PDBe (MSD-EBI) is related to: Worldwide Protein Data Bank (wwPDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: MINAS - Metal Ions in Nucleic AcidS is related to: PDBj - Protein Data Bank Japan has parent organization: University of California at San Diego; California; USA has parent organization: Rutgers University; New Jersey; USA is parent organization of: RCSB PDB Software Tools is parent organization of: Protein Data Bank Markup Language is parent organization of: Ligand Expo works with: CellPhoneDB |
NIH ; DOE ; NSF DBI-1338415 |
PMID:12037327 | Public, Acknowledgement requested | nif-0000-00135, SCR_017379, r3d100010327 | http://www.rcsb.org, http://www.pdb.org, | http://www.rcsb.org/pdb/ | SCR_012820 | RCSB, Research Collaboratory for Structural Bioinformatics Protein Data Bank, The Protein Data Bank, PDB, Protein Databank, RCSB Protein Data Bank, Protein Data Bank | 2026-08-01 12:04:51 | 9870 | |||
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MATCONT and CL MATCONT: Continuation Software in Matlab Resource Report Resource Website 10+ mentions |
MATCONT and CL MATCONT: Continuation Software in Matlab (RRID:SCR_012822) | software resource, software application, data processing software, simulation software | MATCONT is a graphical MATLAB package for the interactive numerical study of parameterized dynamical systems. It is developed in parallel with the command line continuation toolbox CL_MATCONT and with the command line continuation toolbox CL_MATCONTM for the interactive numerical study of parameterized maps and iterates of maps. MATCONT and CL_MATCONT allow the numerical continuation of equilibria, limit cycles and homoclinic orbits, detection of codimension 1 and 2 bifurcations, continuation of the codimension 1 bifurcations and computation of their normal forms. For equilibria normal form coefficients of codimension 2 bifurcations are also computed, as well as switching to the codimension 1 curves in codimension 2 points. CL_MATCONTM provides similar facilities for maps and iterates of maps, including normal form coefficients of codimension 2 bifurcations and continuation of homoclinic and heteroclinic connections and tangencies of such connections. | dynamical system, bifurcation, map, neuroinformatics, normal form, simulation, software | nif-0000-00165 | SCR_012822 | MATCONT | 2026-08-01 12:04:52 | 25 | ||||||||||
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DEXSeq Resource Report Resource Website 500+ mentions |
DEXSeq (RRID:SCR_012823) | DEXSeq | software resource | Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
OMICS_01329, biotools:dexseq | https://bio.tools/dexseq | SCR_012823 | 2026-08-01 12:04:41 | 506 | ||||||||
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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 | 2026-08-01 12:04:43 | 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 | 2026-08-01 12:04:41 | 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 | 2026-08-01 12:04:52 | 428 | ||||||||
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minfi Resource Report Resource Website 100+ mentions |
minfi (RRID:SCR_012830) | minfi | data visualization software, data analysis software, software application, software resource, data processing software | 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 | 2026-08-01 12:04:41 | 390 | ||||||
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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 | 2026-08-01 12:04:40 | 4 | ||||||||||
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RepeatMasker Resource Report Resource Website 5000+ 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 | 2026-08-01 12:04:42 | 9750 | ||||||||
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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) | topical portal, data or information resource, 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 | 2026-08-01 12:04:52 | 11 | ||||||||||
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affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | data processing software, data analysis 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 | 2026-08-01 12:04:52 | 2996 | ||||
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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, portal, research forum portal, topical portal, disease-related 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 | 2026-08-01 12:04:41 | 0 | |||||||||||
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sva package Resource Report Resource Website 50+ 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 | 2026-08-01 12:04:40 | 82 | |||||||||
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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 | 2026-08-01 12:04:41 | 26 | |||||||||||
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National Institute of General Medical Sciences Resource Report Resource Website 100+ 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 | 2026-08-01 12:04:52 | 417 |
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