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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PeakAnalyzer Resource Report Resource Website 1+ mentions |
PeakAnalyzer (RRID:SCR_001194) | PeakAnalyzer | software resource | A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution. | genome, chip, signal peak, binding site, modification site, enrichment loci, peak region, sequence, motif, chip-seq, chip-chip, c++, java, linux, mac os x, windows, bed, gtf, annotation, r, high-throughput sequencing, chromatin binding, modification loci, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:20691053 | Free, Available for download, Freely available | biotools:peakanalyzer, OMICS_02156 | https://bio.tools/peakanalyzer | SCR_001194 | 2026-08-01 12:01:34 | 3 | ||||||
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BreakSeq Resource Report Resource Website 1+ mentions |
BreakSeq (RRID:SCR_001186) | BreakSeq | software resource | Software for scanning reads from short-read sequenced genomes against a human breakpoint library to accurately identify structural variants (SVs). The library of breakpoints at nucleotide resolution were assembled from collating and standardizing ~2,000 published structural variants (SVs). For each breakpoint, its ancestral state (through comparison to primate genomes) was inferred and its mechanism of formation (e.g., nonallelic homologous recombination, NAHR). | structural variant, breakpoint, nucleotide, fasta, gff, bowtie, genomic variation, junction mapping, insertion sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:20037582 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:breakseq, OMICS_02168 | https://bio.tools/breakseq | SCR_001186 | Breakpoint Library and BreakSeq | 2026-08-01 12:01:24 | 1 | |||||
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Bioinformatics Experts Resource Report Resource Website |
Bioinformatics Experts (RRID:SCR_001485) | Bioinformatics Experts | people resource | Investigators interested in Bioinformatics in Canada including practitioners as well as developers of algorithms, databases or resources. Principal investigators and group leaders from academia, government labs and industry are welcome on this page. All present have an interest in the development of bioinformatics resources in Canada. | bioinformatics | has parent organization: Ontario Institute for Cancer Research | Free, Freely available | nlx_152740 | http://bioinformatics.ca/resources/people | SCR_001485 | bioinformatics.ca Bioinformatics Experts, Bioinformatics Experts in Canada | 2026-08-01 12:01:42 | 0 | ||||||
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FunctSNP Resource Report Resource Website |
FunctSNP (RRID:SCR_000393) | FunctSNP | software resource | An R package for linking SNPs (Single Nucleotide Polymorphisms) to functional knowledge. | single nucleotide polymorphism |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20534127 | Free, Available for download, Freely available | OMICS_01925 | SCR_000393 | FunctSNP - Linking SNPs to functional knowledge | 2026-08-01 12:01:16 | 0 | ||||||
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BrainNet Europe Sampling Protocols Resource Report Resource Website |
BrainNet Europe Sampling Protocols (RRID:SCR_000484) | BNE Sampling protocols | protocol | Sampling protocols produced by the BrainNet Europe Consortium generally with five types of dissection and brain processing procedures defined in all disease related protocols. * Fresh brain dissection * Fresh brain processing * Dissection of formalin-fixed brain * Histology and immunohistochemistry * Processing fresh brain | dna preservation, rna preservation, protein preservation, macrodissection, microdissection, tissue sampling, brain banking, dissection, brain processing, brain, fresh, formalin-fixed, histology, immunohistochemistry | has parent organization: BrainNet Europe | Dementia, Depressive Disorder, Schizophrenia, Motor Neuron Disease, Neurodegenerative disease | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158157 | SCR_000484 | 2026-08-01 12:01:14 | 0 | |||||||
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Heptares Therapeutics Resource Report Resource Website |
Heptares Therapeutics (RRID:SCR_000499) | commercial organization | A drug discovery company focused on small-molecule drugs targeting G-protein-coupled receptors (GPCRs), the largest family of druggable targets. Heptares creates new medicines targeting previously undruggable or challenging GPCRs, a superfamily of receptors linked to many diseases. They are pioneering a structure-based drug design approach to GPCRs, leveraging proprietary technologies for protein stabilization, structure determination, and fragment-based discovery. Their partners include Cubist, MorphoSys, AstraZeneca, MedImmune and Takeda. Their objective is to build a broad pipeline of novel medicines to transform the treatment of serious diseases, including Alzheimer's disease, schizophrenia, diabetes, ADHD and chronic migraine. | g-protein coupled receptor, small molecule, drug, biotechnology, medicine, antibody, drug discovery | is related to: Kinetics for Drug Discovery | Alzheimer's disease, Schizophrenia, Diabetes, Attention deficit-hyperactivity disorder, Chronic migraine | nlx_158498, grid.450873.d, ISNI: 0000 0004 0456 4700 | https://ror.org/051fk5x88 | SCR_000499 | Heptares Therapeutics Limited, Heptares Therapeutics Ltd, Heptares | 2026-08-01 12:01:14 | 0 | |||||||
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AlzProtect Resource Report Resource Website |
AlzProtect (RRID:SCR_000492) | AlzProtect | commercial organization | Commercial organization that develops drug candidates in the field of neurodegenerative diseases and particularly Alzheimer's. Their main objective is the development of a drug against Alzheimer's disease from molecules patented by Inserm and the University of Lille II. | late adult human, drug, molecule, neurodegeneration, medicine, drug development | is related to: PharmaCog | Alzheimer's disease, Aging, Neurodegenerative disease | nlx_158327 | SCR_000492 | Alz Protect, SAS AlzProtect, Alzprotect SAS, AlzProtect - Therapeutic Solutions for Neurodegeneration | 2026-08-01 12:01:23 | 0 | |||||||
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CARTA Resource Report Resource Website 1+ mentions |
CARTA (RRID:SCR_000525) | CARTA | nonprofit organization | A virtual organization that promotes transdisciplinary research into anthropogeny, or the study of human origins. The research interests are broad and include finding the structural and molecular differences between humans and apes, identifying and explaining external mechanisms, and defining the evolutionary origins of humans. The center hosts symposia as well as visiting professors for the anthropogeny graduate program. | anthropogeny, anthropology, human, origin, graduate, ape, research, structural, molecular |
has parent organization: University of California at San Diego; California; USA is parent organization of: MOCA is parent organization of: CARTA Libraries |
Mathers Foundation ; Donations |
nlx_51231 | SCR_000525 | Center for Academic Research and Training in Anthropogeny, Center for Academic Research & Training in Anthropogeny | 2026-08-01 12:01:15 | 1 | |||||||
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MetaDrug Resource Report Resource Website 1+ mentions |
MetaDrug (RRID:SCR_000461) | MetaDrug | commercial organization | A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization | pharmacology, compound, pathway, target, metabolite, prediction, toxicity, indication, metabolism, gene, protein, analysis, drug effect | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01584 | SCR_000461 | 2026-08-01 12:01:21 | 1 | ||||||||
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VariantAnnotation Resource Report Resource Website 1+ mentions |
VariantAnnotation (RRID:SCR_000074) | VariantAnnotation | software resource | Software package to annotate variants, compute amino acid coding changes, and predict coding outcomes. | annotation, genetic variant, data import, genetics, high throughput sequencing, snp, sequencing |
is listed by: OMICtools is related to: CRAN has parent organization: Bioconductor has parent organization: Fred Hutchinson Cancer Center |
PMID:24681907 | Free, Available for download, Freely available | OMICS_02073 | SCR_000074 | VariantAnnotation - Annotation of Genetic Variants | 2026-08-01 12:01:07 | 8 | ||||||
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RNAmotifs Resource Report Resource Website 1+ mentions |
RNAmotifs (RRID:SCR_000263) | RNAmotifs | software resource | Software that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. | rna, motif |
is listed by: OMICtools has parent organization: Bitbucket |
OMICS_02287 | https://bitbucket.org/rogrro/rna_motifs | SCR_000263 | rna_motifs, rna motifs | 2026-08-01 12:01:12 | 1 | |||||||
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GISTIC Resource Report Resource Website 10+ mentions |
GISTIC (RRID:SCR_000151) | GISTIC | software resource | Software to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, they improve the estimation of background rates for each category. | somatic copy-number alteration, gene |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Cancer | PMID:21527027 | Free, Available for download, Freely available | OMICS_02296 | SCR_000151 | GISTIC2.0, GISTIC 2.0, GISTIC 2 | 2026-08-01 12:01:10 | 48 | |||||
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JEPETTO Resource Report Resource Website 10+ mentions |
JEPETTO (RRID:SCR_005909) | JEPETTO | software resource | A Cytoscape plugin that performs integrated gene set analysis using information from interaction, pathways and processes databases. The plugin integrates information from three separate web servers specializing in enrichment analysis, pathways expansion and topological matching. It uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes. TopoGSA finds the most similar biological mechanism using the topological features of the interaction network of a user selected gene set. It is also able to suggest genes related to the query gene set using two pathway analysis servers EnrichNet and PathExpand. Both these servers are using a different topological matching algorithms that extends the query gene set with genes from the pathway databases. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results. | gene set enrichment analysis, topological analysis, interaction network, java, enrichment analysis, functional analysis, gene prioritization, integrated analysis, network analysis, interaction, pathway, process, topology, gene |
is listed by: OMICtools has parent organization: Cytoscape has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
PMID:24363376 | GNU General Public License | OMICS_02247 | SCR_005909 | Java Enrichment of Pathways Extended To Topology | 2026-08-01 12:03:00 | 15 | ||||||
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James S. McDonnell Foundation Resource Report Resource Website 50+ mentions |
James S. McDonnell Foundation (RRID:SCR_006341) | JSMF | institution | Supports research and scholarship to improve the quality of life by providing funding for grants in three program areas: studying complex systems, understanding human cognition, and mathematical and complex systems approaches for brain cancer. Types of awards include Fellowship Awards, Scholar Awards, and Collaborative Awards. * Studying Complex Systems: This program supports scholarship and research directed toward the development of theoretical and mathematical tools that can be applied to the study of complex, adaptive, nonlinear systems. It is anticipated that research funded in this program will address issues in fields such as biology, biodiversity, climate, demography, epidemiology, technological change, economic development, governance, or computation. * Understanding Human Cognition: This program supports research studying how neural systems are linked to and support cognitive functions and how cognitive systems are related to an organism's (preferably human) observable behavior. Studies with model organisms should justify why such models were selected and how data obtained from models advances our understanding of human cognition. * Mathematical & Complex Systems Approaches for Brain Cancer: (Collaborative Activity Awards grant type only.) Despite some recent cause for optimism for advancing the clinical treatment of brain cancers, for many patients brain tumor remains a devastating diagnosis. Progress against this disease has been stymied by limited understandings of the molecular, metabolic, and physiological characteristics of human brain cancers across multiple temporal and spatial scales and by the failure of many preclinical models to predict patient responses. | grant, scholarship, cognition, human cognition, human, brain, award, complex system, cancer, biology, biodiversity, climate, demography, epidemiology, technological change, economic development, governance, computation, neural system, behavior, clinical | Brain cancer, Etc. | ISNI: 0000 0004 0612 0441, nlx_152052, grid.453017.4, Crossref funder ID: 100000913, Wikidata: Q6142668 | https://ror.org/03dy4aq19 | SCR_006341 | McDonnell Foundation | 2026-08-01 12:03:07 | 65 | |||||||
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Congressionally Directed Medical Research Program Resource Report Resource Website 10+ mentions |
Congressionally Directed Medical Research Program (RRID:SCR_006456) | CDMRP | nonprofit organization | Fund the best research to eradicate diseases and support the warfighter to benefit the American Public. They promote innovative research, recognizing untapped opportunities, creating partnerships, and guarding the public trust. Research Program topics include: * Amyotrophic Lateral Sclerosis * Autism * Bone Marrow Failure * Breast Cancer * Defense Medical Research and Development Program * Duchenne Muscular Dystrophy * Gulf War Illness * Lung Cancer * Multiple Sclerosis * Neurofibromatosis * Ovarian Cancer * Peer Reviewed Cancer * Peer Reviewed Medical * Peer Reviewed Orthopaedic * Prostate Cancer * Psychological Health / Traumatic Brain Injury * Spinal Cord Injury * Tuberous Sclerosis Complex | grant, funding, one mind tbi, one mind ptsd, medical, medical research, psychological health, orthopedic, peer review, biomedical |
is related to: NIDDK Information Network (dkNET) has parent organization: U.S. Department of Defense |
Amyotrophic Lateral Sclerosis, Autism, Bone marrow failure, Breast cancer, Duchenne muscular dystrophy, Gulf War Illness, Lung cancer, Multiple Sclerosis, Neurofibromatosis, Ovarian cancer, Cancer, Prostate cancer, Traumatic brain injury, Spinal cord injury, Tuberous sclerosis complex | United States Department of Defense | nif-0000-00443, grid.496791.4, Crossref funder ID: 100000090, ISNI: 0000 0000 9367 6288, Wikidata: Q45134126 | https://ror.org/03g2zjp07 | SCR_006456 | DOD CDMRP | 2026-08-01 12:03:08 | 48 | |||||
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Roslin Institute Resource Report Resource Website 1+ mentions |
Roslin Institute (RRID:SCR_006533) | Roslin | institution | World class research center that undertakes top-class basic and translational science to tackle some of the most pressing issues in animal health and welfare, their implications for human health and for the role of animals in the food chain. Roslin provides holistic solutions to global challenges in human and veterinary medicine and the livestock industry. Its mission is to gain fundamental understanding of genetic, cellular, organ and systems bioscience underpinning common mechanisms of animal development and pathology, and to drive this into prevention and treatment of important veterinary diseases and develop sustainable farm animal production systems. The Roslin Institute aims to enhance the lives of animals and humans through world class research in animal biology. The principal objectives are to: * Enhance animal health and welfare through knowledge of genetic factors affecting resistance to disease. * Enhance sustainability and productivity of livestock systems and food supply chains through understanding of reproductive and developmental biology. * Enhance food safety by understanding interactions between disease causing organisms and animals. * Enhance human health through an understanding of basic mechanisms of health and disease and comparative biology of animal species. * Identify of new and emerging zoonoses and understand how pathogens might cross from animals to humans. * Enhance quality of life for animals by studying the mechanisms and behaviors associated with optimizing their environment and life experiences. |
has parent organization: University of Edinburgh Royal (Dick) School of Veterinary Studies; Scotland; United Kingdom is parent organization of: ArkDB - Genomes For The Rest of Us is parent organization of: ARK-Genomics: Centre for Functional Genomics is parent organization of: Pig Genome Mapping |
BBSRC | ISNI: 0000 0000 9166 3715, grid.482685.5, nlx_83761, Wikidata: Q1633976 | https://ror.org/01920rj20 | SCR_006533 | 2026-08-01 12:03:11 | 2 | ||||||||
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Urologic Diseases in America Resource Report Resource Website |
Urologic Diseases in America (RRID:SCR_006644) | UDA | human subject report | A report incorporating current and retrospective data on all aspects of the epidemiology, practice patterns, costs, and impact of urologic diseases in the United States and is intended for use by public officials, nongovernment organizations, the media, academic researchers, health professionals, and the public. The UDA compendium consists of data tables annotated in chapters that amplify the data analyses. The objectives of the UDA project include: secondary data analyses of: changes in the overall healthcare burden for individual urologic diseases, in physician practice patterns for each urologic disease, and in demographics of persons with urologic disease, the impact of specific urologic diseases, especially diseases of the prostate, on the minority populations of the U.S., and documentation of new and evolving therapies for urologic disease and their cost. | epidemiology, urology, diagnosis, risk factor, prevalence, treatment, urological disease, report, practice pattern, data table, data analysis, prostate |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources has parent organization: National Kidney and Urologic Diseases Information Clearinghouse |
Urologic disease | National Institute of Diabetes and Digestive and Kidney Diseases | Public, Acknowledgement requested | nlx_152720 | SCR_006644 | Urologic Diseases in America Compendium, UDA Compendium | 2026-08-01 12:03:16 | 0 | |||||
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Brain Injury Association of America Resource Report Resource Website 1+ mentions |
Brain Injury Association of America (RRID:SCR_006639) | BIAA | nonprofit organization | The country''s oldest and largest nationwide brain injury advocacy organization. We are dedicated to increasing access to quality health care and raising awareness and understanding of brain injury through advocacy, education and research. With a nationwide network of more than 40 chartered state affiliates and hundreds of local chapters and support groups, we provide help, hope and healing for individuals who live with brain injury, their families and the professionals who serve them. Brain injury is not an event or an outcome. It is the start of a misdiagnosed, misunderstood, under-funded neurological disease. Individuals who sustain brain injuries must have timely access to expert trauma care, specialized rehabilitation, lifelong disease management and individualized services and supports in order to live healthy, independent and satisfying lives. | brain, injury, prevention, trauma, traumatic brain injury, brain injury, neurological disease, trauma | Brain injury, Neurological disease | grid.454415.5, ISNI: 0000 0004 0493 9605, nif-0000-10178 | https://ror.org/00mebz780 | SCR_006639 | 2026-08-01 12:03:11 | 1 | ||||||||
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Dissociation Experiences Scale Resource Report Resource Website |
Dissociation Experiences Scale (RRID:SCR_000175) | DES | material resource, assessment test provider | Assessment scale that is a 28 question self test used to screen patients for dissociative identity disorder (formerly called Multiple Personality Disorder). The 28 questions ask the patient about their experiences and their daily life and how often certain events happen. | dissociation | Dissociative identity disorder | Free | nlx_157837 | SCR_000175 | 2026-08-01 12:10:30 | 0 | ||||||||
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NIH Chronic Prostatitis Symptom Index Resource Report Resource Website |
NIH Chronic Prostatitis Symptom Index (RRID:SCR_001482) | CPSI, NIH-CPSI | material resource, assessment test provider | Questionnaire developed by physicians in NIDDK's Chronic Prostatitis Collaborative Research Network that can help physicians to accurately measure the severity of prostatitis symptoms and their impact on a patient's lifestyle. The CPSI questionnaire assesses pain, urination, and the effect of chronic prostatitis on daily activities. With this information, researchers and physicians can reliably evaluate whether potential treatments are working. The questionnaire was originally published in the Journal of Urology in August 1999 (Vol. 162, pages 369-375). It is available as a PDF document in English, Spanish, German and Korean. | pain, symptom, quality of life, male | is listed by: NIDDK Information Network (dkNET) | Prostatitis | NIDDK | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152732 | SCR_001482 | Chronic Prostatitis Symptom Index, National Institutes of Health Chronic Prostatitis Symptoms Index | 2026-08-01 12:10:44 | 0 |
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