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https://github.com/kaizhang/SnapATAC2

Software Python/Rust package for single-cell epigenomics analysis.

Proper citation: SnapATAC2 (RRID:SCR_026622) Copy   

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https://github.com/Yonghao-Holden/TEProf3

Software pipeline to detect Transposable Elements transcripts. Used to identify TE-derived promoters and transcripts using transcriptomic data from multiple sources, including short-read RNA-seq data, long-read RNA-seq data and single cell RNA-seq data.

Proper citation: TEProf3 (RRID:SCR_027288) Copy   

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https://github.com/smorabit/hdWGCNA

Software R package for performing weighted gene co-expression network analysis in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics.

Proper citation: hdWGCNA (RRID:SCR_027496) Copy   

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https://github.com/atakanekiz/CIPR-Package

Software R package for annotating cell clusters in scRNAseq data.

Proper citation: CIPR-Package (RRID:SCR_027697) Copy   

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http://www.adgenetics.org/

Consortium to conduct genome-wide association studies (GWAS) to identify genes associated with an increased risk of developing late-onset Alzheimer''''s disease (LOAD). The goal of the ADGC is to identify genetic variants associated with risk for AD. It plans to do this through the following collaborative goals: # Identify genes responsible for AD susceptibility # Identify AD sub-phenotype genes rate-of-progression plaque / tangle load / distribution biomarker variability # Generate a genetic data resource for the AD research community Data generated by ADGC is available at the following website: https://www.niagads.org/content/alzheimers-disease-genetics-consortium-adgc-collection

Proper citation: Alzheimers Disease Genetics Consortium (RRID:SCR_004004) Copy   

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https://www.uab.edu/medicine/alzheimers/

The UAB Alzheimer's Disease Center provides comprehensive treatment for Alzheimer's patients while also promoting research for the prevention and cure of Alzheimer's disease and related disorders. The ADC is an interdisciplinary program of scientists working in areas including neurology, psychiatry, genetics, and psychology. The Center provides comprehensive treatment and promotes research for the prevention and/or cure of Alzheimer's disease and other related disorders with memory loss and impaired cognition. A major emphasis of research is the maintenance of a clinical research database comprised of neurological, medical, and neuropsychological test data from participants seen in the ADRC Clinical study since 1999, many of whom have been followed for several years in the study.

Proper citation: UAB Alzheimer's Disease Center (RRID:SCR_004305) Copy   

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http://www.rad.upenn.edu/sbia/braid/braid_web/index.html

Large-scale archive of normalized digital spatial and functional data with an analytical query mechanism. One of its many applications is the elucidation of brain structure-function relationships. BRAID stores spatially defined data from digital brain images which have been mapped into normalized Cartesian coordinates, allowing image data from large populations of patients to be combined and compared. The database also contains neurological data from each patient and a query mechanism that can perform statistical structure-function correlations. The project is developing database technology for the manipulation and analysis of 3-dimensional brain images derived from MRI, PET, CT, etc. BRAID is based on the PostgreSQL server, an object/relational DBMS, which allows a standard relational DBMS to be augmented with application-specific datatypes and operators. The BRAID project is adding operations and datatypes to support querying, manipulation and analysis of 3D medical images, including: * Image Datatypes: BRAID supports a family of 3D image datatypes, each having an abstract type and an implementation type. Abstract types include boolean (for regions of interest), integer, float, vector (for representing morphological changes), tensor (for representing derivatives and standard deviations of vector images) and color. Implementation types at present include line-segment format and voxel array. * Image Operators: BRAID supports addition of images, multiplication (which is interpreted as intersection for boolean images), coercion of an image''s abstract or implementation type to another value, and determination of volumes of regions of interest. * Statistical Operators: A chi-squared test has been added to SQL as an aggregate operator on pairs of boolean values. * Web Interface: A general-purpose Web gateway allows the results of queries that return computed images to be displayed. You can download the BRAID source code 2.0. This version is developed under postgreSQL 7.3.4., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BRAID (RRID:SCR_008702) Copy   

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http://med.emory.edu/ADRC/index.html

An Alzheimer's research center which focuses on mild cognitive impairment and early diagnosis and treatment of memory disorders. The Center hosts clinical trials in which the public can participate. Its resources for scientists include a tissue and biospecimen banking facility, the Emory neurology database, and research seminars.

Proper citation: Emory Alzheimer's Disease Research Center (RRID:SCR_008761) Copy   

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http://www.alzresearch.org/index.cfm

A Alzheimer's Disease Research Center (ADRC) whose goal is to conduct basic and clinical research aimed at understanding Alzheimer's disease. The Center enrolls a variety of individuals for clinical trials, evaluation and follow-up, including: normal control subjects, individuals with mild memory problems, and patients diagnosed with Alzheimer's Disease or related dementias. Researchers can request data and specimens obtained from ADRC subjects. These include blood or DNA, brain specimens, and cross-sectional or longitudinal clinical and cognitive data, all from ADRC subjects.

Proper citation: Johns Hopkins Alzheimer's Disease Research Center (RRID:SCR_008757) Copy   

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http://www.bri.ucla.edu/research/resources

Brain bank resources which include postmortem human frozen brain tissue and matched cerebrospinal fluid (CSF) and blood available for scientists to search for etiopathogeneses of human disease. The National Neurological Research Specimen Bank and the Multiple Sclerosis Human Neurospecimen Bank maintains a collection of quick frozen and formalin fixed postmortem human brain tissue and frozen cerebrospinal fluid from patients with neurological diseases, including Alzheimer's Disease, amyotrophic lateral sclerosis, depressive disorder/suicide, and epilepsy, among others. Diagnoses are documented by clinical medical records and gross/microscopic neuropathology. The Neuropathology Laboratory at the UCLA Medical Center maintains a bank of frozen, formalin and paraformaldehyde-fixed and paraffin-embedded postmortem human brain tissues and frozen cerebrospinal fluid (CSF) from patients who die with Alzheimer's disease and other dementing and degenerative illnesses, as well as control materials removed in a similar fashion from patients who are neurologically normal.

Proper citation: Brain Research Institute Biobank Resources (RRID:SCR_008756) Copy   

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http://mayoresearch.mayo.edu/mayo/research/dickson_lab/

A brain bank and laboratory focused on memory and motor disorders. Brains are sent to the laboratory for diagnosis and research for the State of Florida Alzheimer Disease Initiative and for the Society for Progressive Supranuclear Palsy. As part of this brain banking function, fixed and frozen brain samples are obtained at autopsy and sent to the laboratory for diagnostic evaluation and for various types of research studies. The major types of analyses performed on the brain samples include neuro-histology, immunohistochemistry, confocal microscopy, electron microscopy and image analysis, as well as immunoassays. The latter are based upon Western blotting and enzyme linked immunoassays. The laboratory has a specific interest in the interface between normal aging and Alzheimer's disease, as well as in non-Alzheimer's degenerative disorders such as Lewy body dementia, corticobasal degeneration, progressive supranuclear palsy and frontotemporal dementia. The primary focus of research on aging is neuropathologic characterization of brains of individuals who had been prospectively and longitudinally evaluated during life. These studies aim to determine differences in a range of biologic parameters in brains of people with normal cognitive, mild cognitive impairment and dementia. Their focus on Parkinson's disease is to identify preclinical Parkinson's disease in order to develop means for early diagnosis.

Proper citation: Mayo Clinic Jacksonville: Neuropathology and Microscopy (RRID:SCR_008753) Copy   

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http://www.mssm.edu/research/centers/alzheimers-disease-research-center/

A research facility and clinical program that is dedicated to the study and the treatment of both normal aging and Alzheimer's disease. This facility will accommodate requests for its resources (for example, data or tissue) from investigators that are not funded by the ADRC. Their team is composed of experts in geriatrics, geriatric psychiatry and psychology, neurology, pathology, and radiology. All team members work to provide services to those with memory disorders. This center sponsors educational programs for healthcare professionals and community groups. Data from the ADRC cores are available to all ADRC investigators after approval from the PI who collected the data. Data generated by the ADRC cores are communicated to the National Alzheimer's Coordinating Center (NACC) and can be available through them. Tissue can be distributed after approval of the Tissue Allocation Committee, and can be used for further research.

Proper citation: Mount Sinai Alzheimer's Disease Research Center (RRID:SCR_008780) Copy   

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http://depts.washington.edu/adrcweb/

Research center investigating the basic mechanisms underlying the development of Alzheimer's disease and related disorders, directing particular attention to biomarkers and experimental new treatments. They also continue to search for genetic risk factors underlying Alzheimer's disease (AD). Their main priorities are to find causes, effective treatments, and prevention strategies. Their investigators also are partnering with other Alzheimer's Centers across the country to evaluate promising new medications and other treatments for AD. The ultimate goal of their basic and clinical studies is to improve patient care and function, and improve the quality of life for both the patient and the caregiver. ADRC Cores: * Administration * Clinical Core * Satellite Core * Data Management & Biostatistics * Neuropathology Core * Education & Information Transfer * Genetics

Proper citation: University of Washington Alzheimers Disease Research Center (RRID:SCR_008814) Copy   

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http://www.utsouthwestern.edu/education/medical-school/departments/neurology/programs/alzheimers-disease-center/index.html

A center dedicated to discovering treatments and providing preventative measures for Alzheimer's Disease. Research is strongly focused on brain changes in regards to healthy aging, mild cognitive impairment and other disorders, such as dementia. It aims to improve diagnostic measures and care giving techniques, discover more effective medical interventions, and understand the etiology of the disease and find an eventual cure. The center provides diagnostic evaluations of adult memory problems, as well as the opportunity to participate in clinical research to aid in finding better Alzheimer's treatments.

Proper citation: University of Texas Southwestern Medical Center - Alzheimer's Disease Center (RRID:SCR_008836) Copy   

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http://tools.researchonresearch.org/dodsg/web/WebDatabaseHTML.php?service=detail&id=64

THIS RESOURCE IS NO LONGER IN SERVICE, documented on Septemeber 02, 2014. Through a collaborative effort with experts in doctor-elderly patient interaction who participated in the development of ADEPT, a database of approximately 435 audio and video tapes of visits of patients age 65 and older (n=46) to their primary physician was established for testing ADEPT and for access by medical educators and researchers. Data associated with each tape include reason for visit, physician characteristics (age, race, gender), patient characteristics (age, race, gender), companion characteristics (age, race, gender), and length of doctor-patient relationship. Through a collaborative effort with experts in doctor-elderly patient interaction who participated in the development of ADEPT, a database of approximately 435 audio and video tapes of visits of patients age 65 and older (n=46) to their primary physician was established for testing ADEPT and for access by medical educators and researchers. Data associated with each tape include reason for visit, physician characteristics (age, race, gender), patient characteristics (age, race, gender), companion characteristics (age, race, gender), and length of doctor-patient relationship. Patient visits to their primary physician were videotaped at four sites: an academic medical center in the Midwest, an academic medical center in the Southwest, a suburban managed care medical group, and an urban group of physicians in independent practice. Repeat visits between the same doctor and patient were taped for 19 patients resulting in 48 tapes of multiple visits. Patients were recruited in the waiting room for a convenience sample. Before the visit, patients provided demographic data and completed a global satisfaction form. Following the visit, patients completed the SF-36, and the ABIM for patient satisfaction. Two weeks following the visit, patients were contacted by telephone and asked about their understanding, compliance and their utilization of health services over the past year. At twelve months, patients were contacted by telephone for administration of the SF-36, the global satisfaction form, and the utilization of health services survey. Data Availability: Archived at the Saint Louis University School of Medicine Library. Interested researchers and medical educators should contact the PI, Mary Ann Cook, JVCRadiology (at) sbcglobal.net * Dates of Study: 1998-2001 * Study Features: Longitudinal, Anthropometric Measures * Sample Size: 46

Proper citation: ADEPT - Assessment of Doctor-Elderly Patient Encounters (RRID:SCR_008901) Copy   

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http://trans.nih.gov/bmap/index.htm

The Brain Molecular Anatomy Project is a trans-NIH project aimed at understanding gene expression and function in the nervous system. BMAP has two major scientific goals: # Gene discovery: to catalog of all the genes expressed in the nervous system, under both normal and abnormal conditions. # Gene expression analysis: to monitor gene expression patterns in the nervous system as a function of cell type, anatomical location, developmental stage, and physiological state, and thus gain insight into gene function. In pursuit of these goals, BMAP has launched several initiatives to provide resources and funding opportunities for the scientific community. These include several Requests for Applications and Requests for Proposals, descriptions of which can be found in this Web site. BMAP is also in the process of establishing physical and electronic resources for the community, including repositories of cDNA clones for nervous system genes, and databases of gene expression information for the nervous system. Most of the BMAP initiatives so far have focused on the mouse as a model species because of the ease of experimental and genetic manipulation of this organism, and because many models of human disease are available in the mouse. However, research in humans, other mammalian species, non-mammalian vertebrates, and invertebrates is also being funded through BMAP. For the convenience of interested investigators, we have established this Web site as a central information resource, focusing on major NIH-sponsored funding opportunities, initiatives, genomic resources available to the research community, courses and scientific meetings related to BMAP initiatives, and selected reports and publications. When appropriate, we will also post initiatives not directly sponsored by BMAP, but which are deemed relevant to its goals. Posting decisions are made by the Trans-NIH BMAP Committee

Proper citation: BMAP - Brain Molecular Anatomy Project (RRID:SCR_008852) Copy   

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http://gero.usc.edu/CBPH/network/index.shtml

A network to improve measurement of biological risk for late life health outcomes in large representative samples of populations. Activities of the network include designing and carrying out a series of focused meetings, interactive activities, workshops, and pilot projects to harmonize and develop measurement of biological risk in populations. This project will improve the methods of measuring health used in populations and improve comparability of results over time and across studies, which is important for monitoring population health. Biological risk represents objective measurement of major dimensions of population health. The level of risk can indicate the health of the population, need for health care treatment in a population, and the effectiveness of that treatment in controlling risk or delaying disease progression, and death. The measurement of biological risk in large populations often requires adoption of methods not used in laboratory settings. The overarching goal of the network is to promote interdisciplinary research that clarifies the biological paths to health outcomes that can be measured or monitored in population surveys. The network will address the following questions: * What array of biological markers can be included reliably and validly in population studies in order to better monitor health and predict health outcomes at the older ages? * What are the best methods of collecting biological risk information under a variety of circumstances? * What are the best methods for processing the biological risk information collected? * What methods of harmonization will allow us to compare biological risk across studies? * What are the best approaches to measurement of cumulative biological risk or dimensions of biological risk for a variety of health outcomes in a variety of settings? * What are the best approaches in including indicators of genetic risk for complex diseases and conditions into data from population-based surveys? * How do we best capture indicators of life-long social, psychological and economic conditions along with lifelong biological risk to explain later life health outcomes? * What particular ethical issues are posed by our linking of biological data to extensive social, psychological, and economic information? A dataset of descriptions of Selected Population Studies with Biomarkers is available.

Proper citation: Biomarker Network (RRID:SCR_008951) Copy   

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http://senselab.med.yale.edu/ordb/

Database of vertebrate olfactory receptors genes and proteins. It supports sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. The database also incorporates a broad range of chemosensory genes and proteins, including the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfaction receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), and fungal pheromone receptors (FPRs). ORDB currently houses chemosensory receptors for more than 50 organisms. ORDB contains public and private sections which provide tools for investigators to analyze the functions of these very large gene families of G protein-coupled receptors. It also provides links to a local cluster of databases of related information in SenseLab, and to other relevant databases worldwide. The database aims to house all of the known olfactory receptor and chemoreceptor sequences in both nucleotide and amino acid form and serves four main purposes: * It is a repository of olfactory receptor sequences. * It provides tools for sequence analysis. * It supports similarity searches (screens) which reduces duplicate work. * It provides links to other types of receptor information, e.g. 3D models. The database is accessible to two classes of users: * General public www users have full access to all the public sequences, models and resources in the database. * Source laboratories are the laboratories that clone olfactory receptors and submit sequences in the private or public database. They can search any sequence they deposited to the database against any private or public sequence in the database. This user level is suited for laboratories that are actively cloning olfactory receptors.

Proper citation: Olfactory Receptor DataBase (RRID:SCR_007830) Copy   

•   Source: SciCrunch Registry

http://www.adrc.pitt.edu/

A research center associated with the University of Pittsburgh that specializes in the diagnosis of Alzheimer's disease and related disorders. The overall objective of the ADRC is to study the pathophysiology of Alzheimer's disease, with the aim of improving the reliability of diagnosis of Alzheimer's and developing effective treatment strategies. Current research foci emphasize neuropsychiatry and neuropsychology, molecular genetics and epidemiology, basic neuroscience, and structural and functional imaging that aid in the diagnosis and treatment of Alzheimer's disease. Specific services at the ADRC include: comprehensive diagnostic evaluation of patients with suspected Alzheimer's disease and other forms of dementia; evaluation of memory, language, judgment, and other cognitive abilities; and education and counseling for patients and families.

Proper citation: University of Pittsburgh Alzheimer Disease Research Center (RRID:SCR_008084) Copy   

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http://www.nia.nih.gov/research/scientific-resources

A resource that provides information on the vast number of resources available from the National Institute of Aging. NIA maintains approximately 150 primates (Macaca mulatta) at four regional primate centers where aging-related research is conducted. NIA also maintains colonies of aged rats and mice that are used for age-related disease research. This resource supports a multi-institutional study, the Interventions Testing Program (ITP), that investigates diets and dietary supplements that extend lifespan, delay disease and avoid dysfunction. NIA is also in charge of a microarray facility which provides filter arrays of 17,000 mouse cDNA clone sets that were developed at the NIA Intramural Research Program Laboratory of Genetics. NIA supports studies that provide biospecimens that can be shared for later research. This resource also helps the C. elegans Genetic Center at the University of Minnesota, which contains 1,000 strains of C. elegans that can be used for aging studies. This resource also provides a searchable database for epidemiological research on aging. There is access to social and behavioral research materials, including books on aging and health, from the research was conducted and supported by NIA. There are links to federal web sites that are further resources for aging research that were supported by NIA.

Proper citation: NIA Scientific Resources (RRID:SCR_008269) Copy   

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