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https://pypi.org/project/SpaGCN/

Software graph convolutional network to integrate gene expression and histology to identify spatial domains and spatially variable genes. SpaGCN integrates information from gene.

Proper citation: SpaGCN (RRID:SCR_025978) Copy   

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https://github.com/cafferychen777/ggpicrust2

Software R package for analyzing and interpreting results of PICRUSt2 functional prediction. Offers range of features, including pathway name/description annotations, advanced differential abundance methods, and visualization of differential abundance results. Used for PICRUSt2 predicted functional profile analysis and visualization.

Proper citation: ggpicrust2 (RRID:SCR_025965) Copy   

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https://github.com/j-rub/scVital

Software tool to embed scRNA-seq data into species-agnostic latent space to overcome batch effect and identify cell states shared between species. Deep learning algorithm for cross-species integration of scRNA-seq data.

Proper citation: scVital (RRID:SCR_026215) Copy   

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https://www.c4r-nih.org

Portal provides information about nationwide study of more than 50,000 individuals to determine factors that predict disease severity and long-term health impacts of COVID-19.

Proper citation: Collaborative Cohort of Cohorts for COVID-19 Research (RRID:SCR_026322) Copy   

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https://github.com/Washington-University/HCPpipelines

Software package as set of tools, primarily shell scripts, for processing multi-modal, high-quality MRI images for the Human Connectome Project. Minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space.

Proper citation: HCP Pipelines (RRID:SCR_026575) Copy   

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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://knightadrc.wustl.edu/professionals-clinicians/request-center-resources/

Provides on request resources including Data: clinical and cognitive measures as well as MRI and amyloid imaging scans; Tissue: frozen brain tissue, paraffin brain sections, antemortem CSF, DNA, fibroblast, dermal fibroblasts, plasma (fasting and non-fasting) and iPSC; Participants: eligible participants may be invited to enroll in research of other investigators after appropriate review. Researchers can use the request portal to review Center guidelines and policies; view available data and tissue; access data tables and codebooks; and submit request for resources.

Proper citation: Washington University School of Medicine Knight ADRC Request Center Resources Core Facility (RRID:SCR_025254) Copy   

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https://github.com/bsml320/Scupa/

Software R package for immune cell polarization assessment of scRNA-seq data. Single-cell unified polarization assessment of immune cells using single-cell foundation model. Used for comprehensive immune cell polarization analysis.

Proper citation: Scupa (RRID:SCR_025755) 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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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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http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03253

Data set from six research sites that examined the feasibility and outcomes of the most promising home and community-based intervention approaches for enhancing family caregiving for Alzheimers Disease (AD) and related disorders (ADRD). A unique feature is the examination of AD burdens and interventions in three ethnic groups (Caucasians, Hispanics, and African Americans). Caregiver/care recipient dyads are entered into the study using standardized eligibility criteria. The dyads are randomized at each intervention site using site-specific procedures. Standardized assessment batteries are administered at baseline, 6, 12, and 18 months. The five general types of REACH interventions are: Individual Information and Support strategies that increase caregivers' understanding of dementia and their particular caregiving situation; Group Support and Family Systems efforts that provide caregivers with multiple forms of social support; Psychoeducational and Skill-Based Training approaches that teach caregivers coping and behavioral management strategies; Home-Based Environmental interventions that modify the home environment's effect on the care recipient and support the caregiver; and Enhanced Technology Systems such as home-centered computer/telephone networks that are designed to reduce caregiver distress and isolation. REACH II was funded in 2001 to test a single multi-component intervention among family caregivers of persons with ADRD, building upon the findings of REACH. Recruitment for REACH II was completed in January 2004 with 642 participants entering the study across 5 participating sites.

Proper citation: Resources for Enhancing Alzheimers Caregiver Health (RRID:SCR_003638) Copy   

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http://www.icpsr.umich.edu/icpsrweb/NACDA/studies/02744/version/1

Data set of a follow-up study (one of four Established Populations for Epidemiologic Studies of the Elderly - EPESE) that obtains information on four primary outcome variables (cognitive status, depression, functional status, and mortality) and four primary independent variables (social support, social class, social location, and chronic illness); and examines the relationships between social factors and chronic disease on the one hand and health outcomes on the other. This data set complements the other three sites providing a population which is both urban and rural and contains approximately equal numbers of black and white participants across a broad socioeconomic base. The Duke site was originally funded by the NIA Epidemiology, Demography and Biometry Program (EDBP) to complete seven waves of data collection (three in-person and four telephone interviews) in order to examine the health of a sample of 4,162 persons aged 65+, and factors that influence their health and use of health services. The cohort was originally interviewed in 1986/87 and followed annually for 6 years thereafter. The study design consisted of a random stratified household sample with an over-sampling of blacks. Questionnaire topics include the following: Demographics, Alcohol Use, Independence, Health condition, Cognition, Personal mastery, Health Service Utilization, Activity of daily living, Social Support, Hearing and Vision, Incontinence, Social Interaction, Weight and Height, Smoking, Religion, Nutrition, Life Satisfaction, Self Esteem, Sleep, Medications, Economic Status, Depression, Life Changes, Blood pressure. National Death Index files have been searched and death certificates obtained for the members of this study. Sample members have been matched with Medicare Part A files to obtain information on hospitalizations, and will be matched on Medicare Part B (outpatient) files. Data from the first wave of the survey is in the public domain and can be obtained from NACDA or from the National Archives, Center for Electronic Records in Washington, DC. * Dates of Study: 1996-1997 * Study Features: Longitudinal, Oversampling * Sample Size: 1986-1988: 4,162 Links: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/02744 * National Archives: http://www.archives.gov/research/electronic-records/

Proper citation: Piedmont Health Survey of the Elderly (RRID:SCR_006349) Copy   

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http://www.ifs.org.uk/ELSA

An interdisciplinary data resource on health, economic position and quality of life as people age. Longitudinal multidisciplinary data from a representative sample of the English population aged 50 and older have been collected. Both objective and subjective data are collected relating to health and disability, biological markers of disease, economic circumstance, social participation, networks and well-being. Participants are surveyed every two years to see how people''s health, economic and social circumstances may change over time. One of the study''s aims is to determine the relationships between functioning and health, social networks, resources and economic position as people plan for, move into and progress beyond retirement. It is patterned after the Health and Retirement Study, a similar study based in the United States. ELSA''s method of data collection includes face-to-face interview with respondents aged 50+; self-completion; and clinical, physical, and performance measurements (e.g., timed walk). Wave 2 added questions about quality of health care, literacy, and household consumption, and a visit by a nurse to obtain anthropometric, blood pressure, and lung function measurements, as well as saliva and blood samples, and to record results from tests of balance and muscle strength. Another new aspect of Wave 2 is the ''Exit Interview'' carried out with proxy informants to collect data about respondents who have died since Wave 1. This interview includes questions about the respondents'' physical and psychological health, the care and support they received, their memory and mood in the last year of their life, and details of what has happened to their finances after their death. Wave 3 data added questions related to mortgages and pensions. The intention is to conduct interviews every 2 years, and to have a nurse visit every 4 years. It also is envisioned that the ELSA data will ultimately be linked to available administrative data, such as death registry data, a cancer register, NHS hospital episodes data, National Insurance contributions, benefits, and tax credit records. The survey data are designed to be used for the investigation of a broad set of topics relevant to understanding the aging process. These include: * health trajectories, disability and healthy life expectancy; * the determinants of economic position in older age; * the links between economic position, physical health, cognition and mental health; * the nature and timing of retirement and post-retirement labour market activity; * household and family structure, social networks and social supports; * patterns, determinants and consequences of social, civic and cultural participation; * predictors of well-being. Current funding for ELSA will extend the panel to 12 years of study, giving significant potential for longitudinal analyses to examine causal processes. * Dates of Study: 2002-2007 * Study Features: Longitudinal, International, Anthropometric Measures * Sample Size: ** 2000-2003 (Wave 1): 12,100 ** 2004-2005 (Wave 2): 9,433 ** 2006-2007 (Wave 3): 9,771 ** 2008-2009 (Wave 4): underway Links * Economic and Social Data Service (ESDS): http://www.esds.ac.uk/longitudinal/about/overview.asp * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00139#scope-of-study

Proper citation: English Longitudinal Study of Ageing (RRID:SCR_006727) Copy   

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http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04432#summary

Data set from a long-term population-based prospective study of non-institutionalized residents (aged 21 or older, or aged 16-21 and older if married) in Alameda County, California investigating social and behavioral risk factors for morbidity, mortality, functioning and health. Questions were asked on marital and life satisfaction, parenting, physical activities, employment, health status, and childhood experiences. Demographic information on age, race, height, weight, education, income, and religion was also collected. Included with this dataset is a separate file (part 2) containing mortality data. With the aging of this cohort, data are becoming increasingly valuable for examining the life-long cumulative effects of social and behavioral factors on a well-characterized population. The first wave collected information for 6,928 respondents (including approximately 500 women aged 65 years and older) on chronic health conditions, health behaviors, social involvements, and psychological characteristics. The 1974 questionnaire was sent to 6,246 living subjects who had responded in 1965, and were able to be located. The third wave provides a follow-up of 2,729 original 1965 and 1974 respondents and examines health behaviors such as alcohol consumption and smoking habits, along with social activities. Also included is information on health conditions such as diabetes, osteoporosis, hormone replacement, and mental illness. Another central topic investigated is activities of daily living (including self-care such as dressing, eating, and shopping), along with use of free time and level of involvement in social, recreational, religious, and environmental groups. The fourth wave is a follow-up to the 1994 panel and examines changes in functional abilities such as self-care activities, employment, involvement in community activities, visiting friends/family, and use of free time since 1994. * Dates of Study: 1965-1999 * Sample Size: 1965: 6,928; 1974: 4,864; 1994: 2,729; 1995: 2,569, 1999: 2,123 * Study Features: Longitudinal Links: * 1965 ICPSR, http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06688 * 1974 ICPSR, http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06838 * 1994 and 1995 ICPSR, http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03083 * 1999 ICPSR, http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04432#summary

Proper citation: Alameda County Health and Ways of Living Study (RRID:SCR_008889) Copy   

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http://www.nber.org/papers/h0038

A dataset to advance the study of life-cycle interactions of biomedical and socioeconomic factors in the aging process. The EI project has assembled a variety of large datasets covering the life histories of approximately 39,616 white male volunteers (drawn from a random sample of 331 companies) who served in the Union Army (UA), and of about 6,000 African-American veterans from 51 randomly selected United States Colored Troops companies (USCT). Their military records were linked to pension and medical records that detailed the soldiers������?? health status and socioeconomic and family characteristics. Each soldier was searched for in the US decennial census for the years in which they were most likely to be found alive (1850, 1860, 1880, 1900, 1910). In addition, a sample consisting of 70,000 men examined for service in the Union Army between September 1864 and April 1865 has been assembled and linked only to census records. These records will be useful for life-cycle comparisons of those accepted and rejected for service. Military Data: The military service and wartime medical histories of the UA and USCT men were collected from the Union Army and United States Colored Troops military service records, carded medical records, and other wartime documents. Pension Data: Wherever possible, the UA and USCT samples have been linked to pension records, including surgeon''''s certificates. About 70% of men in the Union Army sample have a pension. These records provide the bulk of the socioeconomic and demographic information on these men from the late 1800s through the early 1900s, including family structure and employment information. In addition, the surgeon''''s certificates provide rich medical histories, with an average of 5 examinations per linked recruit for the UA, and about 2.5 exams per USCT recruit. Census Data: Both early and late-age familial and socioeconomic information is collected from the manuscript schedules of the federal censuses of 1850, 1860, 1870 (incomplete), 1880, 1900, and 1910. Data Availability: All of the datasets (Military Union Army; linked Census; Surgeon''''s Certificates; Examination Records, and supporting ecological and environmental variables) are publicly available from ICPSR. In addition, copies on CD-ROM may be obtained from the CPE, which also maintains an interactive Internet Data Archive and Documentation Library, which can be accessed on the Project Website. * Dates of Study: 1850-1910 * Study Features: Longitudinal, Minority Oversamples * Sample Size: ** Union Army: 35,747 ** Colored Troops: 6,187 ** Examination Sample: 70,800 ICPSR Link: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06836

Proper citation: Early Indicators of Later Work Levels Disease and Death (EI) - Union Army Samples Public Health and Ecological Datasets (RRID:SCR_008921) Copy   

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http://prehco.rcm.upr.edu/

A dataset that provides researchers and policy makers information about issues affecting the elderly population in Puerto Rico: health status, housing arrangements, functional status, transfers, labor history, migration, income, childhood characteristics, health insurance, use of health services, marital history, mistreat, sexuality, etc. It investigates the characteristics of older adults (aged 60+) through an island-wide cross-sectional sample survey of target individuals and their surviving spouses. The sampling frame was constructed on the basis of an advance release of the 2000 US Census. The population for the study consists of the elderly population (60+) in households in Puerto Rico. The sample design used a multistage probabilistic sample by cluster. All elderly adults who lived in the selected households were eligible. If more than one person was in the target population, one 60+ adult was the target and one was the spouse. Respondents 80+ and males in couples who were both 80+ were oversampled. There were 4,293 targets aged 60+ and 1,444 spouses (all ages) in the first wave. Types of data include demographic; household composition; marital history; Cantrill Scale; mini-mental (designed to measure cognitive capacity of Spanish-speaking Latinos with low levels of education and to provide early indications of dementia); self-reported health status; diagnosed health conditions; childhood conditions; transfers; labor history; migration; housing; assets; Activities of Daily Living; Instrumental Activities of Daily Living; medicines; health insurance and use of health services; family structure; sexuality; anthropometric measures. Project innovations include: (1) the design and test of a new tool for assessing cognition among Spanish speaking elderly of low levels of education, (2) a symptoms section to assess the validity of selected self reported conditions, (3) a modification of the Cantrill''s Ladder Scale, (4) protocols for physical measurements to assess current, as well as past, conditions, and (5) the use of GIS and GPS in the fieldwork supervision and to geocoding the survey data. At this moment PREHCO has completed a second wave to become a longitudinal study. The questionnaire included questions regarding the changing conditions (health, residential, social and economic) of those individuals who responded the first questionnaire. The new questionnaire included novel components: vignettes for health status self-report, a new improved section on disability and dependency, and on labor force participation. We also expanded the section of anthropometry by adding a few measurements and physical efficiency tests. Those participants deceased or institutionalized were interviewed using a proxy. Data Availability: First and second wave data are available for public use through BADGIR, the online data archive at the University of Wisconsin-Madison, at: http://nesstar.ssc.wisc.edu/ * Dates of Study: 2002-2003, 2004-2006 * Study Features: Longitudinal, International, Minority Oversampling, Anthropometric measures * Sample Size: 5,336

Proper citation: Puerto Rican Elderly: Health Conditions (RRID:SCR_008916) Copy   

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http://wwwcf.nlm.nih.gov/hsrr_search/view_hsrr_record_table.cfm?TITLE_ID=475&PROGRAM_CAME=toc_with_source2.cfm

A data set designed to provide a cross-sectional description of health, mental, and social status of the oldest-old segment of the elderly population in Israel, and to serve as a baseline for a multiple-stage research program to correlate demographic, health, and functional status with subsequent mortality, selected morbidity, and institutionalization. Study data are based on a sample of Jewish subjects aged 75+, alive and living in Israel on January 1, 1989, randomly selected from the National Population Register (NPR), a complete listing of the Israeli population maintained by the Ministry of the Interior. The NPR is updated on a routine basis with births, deaths, and in and out migration, and corrected by linkage with census data. The sample was stratified by age (five 5-year age groups: 75-79, 80-84, 85-89, 90-94, 95+), sex, and place of birth (Israel, Asia-Africa, Europe-America). One hundred subjects were randomly selected in each of the 30 strata. However, there were less than 100 individuals of each sex aged 95+ born in Israel, so all were selected for the sample. The total group included 2,891 individuals living both in the community and in institutions. A total of 1,820 (76%) of the 75-94 age group were interviewed during 1989-1992. An additional cognitive exam (Folstein) and a 24-hour dietary recall interview were added in the second round. Kibbutz Residents Sample The kibbutz is a social and economic unit based on equality among members, common property and work, collaborative consumption, and democracy in decision making. There are 250 kibbutzim in Israel, and their population constitutes about 3% of the country''s total population. All kibbutz residents in the country aged 85+, both members and parents, were selected for interviewing, of whom 80.4% (n=652) were interviewed. A matched sample aged 75-84 was selected, and 85.9% (n=674) were successfully interviewed. The original interview took approximately two hours to administer, and collected extensive information concerning the socio-demographic, physical, health, functioning, life events (including Holocaust), depression, mental status, and social network characteristics of the sample. The questionnaire used for kibbutz residents in the follow-up interview is identical to that utilized in the national random sample. Data Availability: Mortality data for both the national and kibbutz samples are available for analysis as a result of the linkage to the NPR file updated as of June 2000. The fieldwork for first follow up was completed as of September 1994 and for the second follow up as of December 2002. The data file of the three phases of the study is ready for analysis. * Dates of Study: 1989-1992 * Study Features: Longitudinal, International * Sample Size: 2,891

Proper citation: Cross-Sectional and Longitudinal Aging Study (RRID:SCR_008903) Copy   

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http://www.rand.org/labor/FLS/MHSS.html

A data set of the health and socioeconomic factors that affect the elderly in Matlab, a region of rural Bangladesh. The survey captures measurements and statistics such as adult survival, health status, health care utilization, resource flows between generations and the impact of community services and infrastructure on adult health care. Data was collected through surveys that touch on four topics: household and individual information; determinants of natural fertility; migration out of the community; and community and provider survey of healthcare and education infrastructure.

Proper citation: Matlab Health and Socio-Economic Survey (RRID:SCR_008942) Copy   

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http://webcache.googleusercontent.com/search?q=cache:srOrfTsktEsJ:https://portal.utpa.edu/portal/page/portal/80C547C751AC1698E04400306EF397E0+&cd=1&hl=en&ct=clnk&gl=us

A dataset of a longitudinal study of over 3,000 Mexican-Americans aged 65 or over living in five southwestern states. The objective is to describe the physical and mental health of the study group and link them to key social variables (e.g., social support, health behavior, acculturation, migration). To the extent possible, the study was modeled after the existing EPESE studies, especially the Duke EPESE, which included a large sample if African-Americans. Unlike the other EPESE studies that were restricted to small geographic areas, the Hispanic EPESE aimed at obtaining a representative sample of community-dwelling Mexican-American elderly residing in Texas, New Mexico, Arizona, Colorado, and California. Approximately 85% of Mexican-American elderly reside in these states and data were obtained that are generalizable to roughly 500,000 older people. The final sample of 3,050 subjects at baseline is comparable to those of the other EPESE studies. Data Availability: Waves I to IV are available through the National Archive of Computerized Data on Aging (NACDA), ICPSR. Also available through NACDA is the ����??Resource Book of the Hispanic Established Populations for the Epidemiologic Studies of the Elderly����?? which offers a thorough review of the data and its applications. All subjects aged 75 or older were interviewed for Wave V and 902 new subjects were added. Hemoglobin A1c test kits were provided to subjects who self-reported diabetes. Approximately 270 of the kits were returned for analyses. Wave V data are being validated and reviewed. A tentative timeline for the archiving of Wave V data is November 2006. Wave VI interviewing and data collection is scheduled to begin in Fall 2006. * Dates of Study: 1993-2006 * Study Features: Longitudinal, Minority oversamples, Anthropometric Measures * Sample Size: ** 1993-4: 3,050 (Wave I) ** 1995-6: 2,438 (Wave II) ** 1998-9: 1,980 (Wave III) ** 2000-1: 1,682 (Wave IV) ** 2004-5: 2,073 (Wave V) ** 2006-7: (Wave VI) Links: * ICPSR Wave 1: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/2851 * ICPSR Wave 2: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/3385 * ICPSR Wave 3: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/4102 * ICPSR Wave 4: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/4314 * ICPSR Wave 5: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/25041 * ICPSR Wave 6: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/29654

Proper citation: Longitudinal Study of Elderly Mexican American Health (RRID:SCR_008941) Copy   

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