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http://hms-dbmi.github.io/scde/index.html

Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.)

Proper citation: SCDE (RRID:SCR_015952) Copy   

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https://www.rdocumentation.org/packages/DGCA/versions/1.0.2

Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix.

Proper citation: Differential Gene Correlation Analysis (RRID:SCR_020964) Copy   

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https://github.com/denisecailab/minian

Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output.

Proper citation: Minian (RRID:SCR_022601) Copy   

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https://imputationserver.sph.umich.edu/index.html#!pages/home

Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.

Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy   

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http://www.grc.nia.nih.gov/

A research program of the NIA which focuses on neuroscience, aging biology, and translational gerontology. The central focus of the program's research is understanding age-related changes in physiology and the ability to adapt to environmental stress, and using that understanding to develop insight about the pathophysiology of age-related diseases. The IRP webpage provides access to other NIH resources such as the Biological Biochemical Image Database, the Bioinformatics Portal, and the Baltimore Longitudinal Study of Aging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Intramural Research Program (RRID:SCR_012734) Copy   

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http://mrtools.mgh.harvard.edu/index.php/TBR

A tool for functional connectivity analysis of fcMRI data that maps functional data from individual sessions onto a priori spatial components from group level parcellations.

Proper citation: Template Based Rotation (RRID:SCR_012157) Copy   

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http://cbl.uh.edu/ORION/

Project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.

Proper citation: ORION (RRID:SCR_010621) Copy   

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http://pklab.med.harvard.edu/scde/pagoda.links.html

Software tool for analyzing transcriptional heterogeneity to detect statistically significant ways in which measured cells can be classified. Used to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells.

Proper citation: PAGODA (RRID:SCR_017099) Copy   

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http://research.mssm.edu/integrative-network-biology/Software.html

Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles.

Proper citation: proMODMatcher (RRID:SCR_017219) Copy   

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https://imputationserver.sph.umich.edu/

Web server to implement whole genotype imputation workflow for efficient parallelization of computationally intensive tasks. Service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity. Used to find haplotype segments and reference panel of sequenced genomes, assign genotypes at untyped markers, improve genome coverage, facilitate comparison and combination of studies that use different marker panels, increase power to detect genetic association, and guide fine mapping.

Proper citation: Michigan Imputation Server (RRID:SCR_017579) Copy   

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https://www.archrproject.com/

Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing.

Proper citation: ArchR (RRID:SCR_020982) Copy   

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https://majiq.biociphers.org/

Software package to detect and quantify local splicing variations (LSV) from RNA-Seq data. Used to automatically detect and downweight outliers in RNA-Seq datasets with replicates for differential splicing (SD) analysis.

Proper citation: MAJIQ (RRID:SCR_016706) Copy   

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https://github.com/HussainiLab/hfoGUI

Graphical user interface to visualize EEG data. The applications can vary from scoring High Frequency Oscillations, to observing Theta and Gamma Synchrony.

Proper citation: hfoGUI (RRID:SCR_016726) Copy   

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http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06718

Data set on the prevalence of self-care behaviors by non-institutionalized older adults. Personal interviews were conducted with 3,485 individuals 65 years of age and older, with oversampling of the oldest old. Questions were asked about the type and extent of self-care behaviors for activities of daily living, management of chronic conditions (through self-care activities, equipment use, and environmental modifications), medical self-care for acute conditions, health promotion/disease preventions, social support, health service utilization, and socio-demographic/economic status. A follow-up study by telephone was conducted in 1994 to continue examination of subjects. Many of the same questions from the baseline were asked, along with questions regarding change in health status since baseline and nursing home visits. For subjects who had been institutionalized since baseline (Part 2), information was gathered (by proxy) regarding demographic status, living arrangements prior to institutionalization, and reasons for institutionalization. For subjects who had died since baseline (Part 3), information was again gathered through interviews with proxies. Questions covered nursing home admissions and date and place of death. In both waves, a proxy was substituted if the subject was hospitalized (or institutionalized since baseline), too ill, cognitively not able to respond, or deceased. Survey data were linked to Medicare/Medicaid health utilization records. The baseline data are archived at NACDA as ICPSR Study No. 6718, and the followup data are archived as ICPSR Study No. 2592 and linkable to the baseline data. * Dates of Study: 1990-1994 * Study Features: Longitudinal * Sample Size: ** 1990-1: 3,485 (Baseline) ** 1994: 2,601 (Followup) Links: * 1990-1991 Baseline ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06718 * 1994 Follow-up ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/02592

Proper citation: National Survey of Self-Care and Aging (RRID:SCR_013456) Copy   

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http://www.ssc.wisc.edu/nsfh/home.htm

A national sample survey dataset covering a wide variety of issues on American family life beginning in 1987-88 and at two subsequent timepoints1992-93 and 2001-03. Topics covered included detailed household composition, family background, adult family transitions, couple interactions, parent-child interactions, education and work, health, economic and psychological well-being, and family attitudes. The first wave interviewed 13,017 respondents, including a main cross-section sample of 9,643 persons aged 19 and over plus an oversample of minorities and households containing single-parent families, step-families, recently married couples, and cohabiting couples. In each household, a randomly selected adult was interviewed. In addition, a shorter, self-administered questionnaire was filled out by the spouse or cohabiting partner of the primary respondent. Interviews averaged about 100 minutes, although interview length varied considerably with the complexity of the respondent''s family history. In 1992-94, an in-person interview was conducted of all surviving members of the original sample, the current spouse or cohabiting partner, and with the baseline spouse or partner in cases where the relationship had ended. Telephone interviews were conducted with focal children who were aged 5-12 and 13-18 at baseline. Short proxy interviews were conducted with a surviving spouse or other relative in cases where the original respondent died or was too ill to interview. A telephone interview was conducted with one randomly selected parent of the main respondent. In 2001-03, telephone interviews were conducted with: Surviving members of the original respondents who had a focal child age 5 or over at baseline; the baseline spouse/partner of these original respondents, whether or not the couple was still together; the focal children who were in the household and aged 5-18 at baselinemost of whom were interviewed at wave 2; and all other original respondents age 45 or older in 2000, and their baseline spouse/partner. Oversamples: Blacks, 9.2%; Mexican-Americans, 2.4%; Puerto Ricans, 0.7% * Dates of Study: 1987-2003 * Study Features: Longitudinal, Minority Oversampling * Sample Size (original respondents): ** Wave I (1987-88): 13,017 ** Wave II (1992-93): 10,007 ** Wave III (2001-03): 8,990 Links: * Wave I (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06041 * Wave II (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06906 * Wave III (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00171

Proper citation: National Survey of Families and Households (RRID:SCR_013388) Copy   

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http://www.diw.de/en/soep

A wide-ranging representative longitudinal study of private households that permits researchers to track yearly changes in the health and economic well-being of older people relative to younger people in Germany from 1984 to the present. Every year, there were nearly 11,000 households, and more than 20,000 persons sampled by the fieldwork organization TNS Infratest Sozialforschung. The data provide information on all household members, consisting of Germans living in the Old and New German States, Foreigners, and recent Immigrants to Germany. The Panel was started in 1984. Some of the many topics include household composition, occupational biographies, employment, earnings, health and satisfaction indicators. In addition to standard demographic information, the GSOEP questionnaire also contains objective measuresuse of time, use of earnings, income, benefit payments, health, etc. and subjective measures - level of satisfaction with various aspects of life, hopes and fears, political involvement, etc. of the German population. The first wave, collected in 1984 in the western states of Germany, contains 5,921 households in two randomly sampled sub-groups: 1) German Sub-Sample: people in private households where the head of household was not of Turkish, Greek, Yugoslavian, Spanish, or Italian nationality; 2) Foreign Sub-Sample: people in private households where the head of household was of Turkish, Greek, Yugoslavian, Spanish, or Italian nationality. In each year since 1984, the GSOEP has attempted to re-interview original sample members unless they leave the country. A major expansion of the GSOEP was necessitated by German reunification. In June 1990, the GSOEP fielded a first wave of the eastern states of Germany. This sub-sample includes individuals in private households where the head of household was a citizen of the German Democratic Republic. The first wave contains 2,179 households. In 1994 and 1995, the GSOEP added a sample of immigrants to the western states of Germany from 522 households who arrived after 1984, which in 2006 included 360 households and 684 respondents. In 1998 a new refreshment sample of 1,067 households was selected from the population of private households. In 2000 a sample was drawn using essentially similar selection rules as the original German sub-sample and the 1998 refreshment sample with some modifications. The 2000 sample includes 6,052 households covering 10,890 individuals. Finally, in 2002, an overrepresentation of high-income households was added with 2,671 respondents from 1,224 households, of which 1,801 individuals (689 households) were still included in the year 2006. Data Availability: The data are available to researchers in Germany and abroad in SPSS, SAS, TDA, STATA, and ASCII format for immediate use. Extensive documentation in English and German is available online. The SOEP data are available in German and English, alone or in combination with data from other international panel surveys (e.g., the Cross-National Equivalent Files which contain panel data from Canada, Germany, and the United States). The public use file of the SOEP with anonymous microdata is provided free of charge (plus shipping costs) to universities and research centers. The individual SOEP datasets cannot be downloaded from the DIW Web site due to data protection regulations. Use of the data is subject to special regulations, and data privacy laws necessitate the signing of a data transfer contract with the DIW. The English Language Public Use Version of the GSOEP is distributed and administered by the Department of Policy Analysis and Management, Cornell University. The data are available on CD-ROM from Cornell for a fee. Full instructions for accessing GSOEP data may be accessed on the project website, http://www.human.cornell.edu/che/PAM/Research/Centers-Programs/German-Panel/cnef.cfm * Dates of Study: 1984-present * Study Features: Longitudinal, International * Sample Size: ** 1984: 12,290 (GSOEP West) ** 1990: 4,453 (GSOEP East) ** 2000: 20,000+ Links: * Cornell Project Website: http://www.human.cornell.edu/che/PAM/Research/Centers-Programs/German-Panel/cnef.cfm * GSOEP ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00131

Proper citation: German Socio-Economic Panel (RRID:SCR_013140) Copy   

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http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04219

A collection of data of an epidemiological study of chronic disease in the oldest old based on information collected from Kaiser Permanente facilities in Northern California (KPNC). The initial sample was drawn from the Kaiser''s active membership lists for the years 1971 and 1980. The sample was restricted to members that had a Multiphasic Health Checkup examination (MHC) within 7 years of the baseline date. The sample was stratified to attain equal numbers of observations (1,000 in each) in three sex-age cells for each cohort: 65-69, 70-79, and 80+. Each cohort was followed for 9 years through existing medical records and computerized hospitalization tapes. Mortality data was collected by matching the sampled data with state Vital Statistics data for an additional 3 years for a total follow-up time of 12 years. Part 1 of the data collections consists of Master Records, which includes information from the morbidity review, in which over 35 chronic conditions or diagnoses were abstracted from the member charts, as well as detailed diagnostic criteria for the major conditions. A prevalence review was done, which included the 4 years prior to the baseline date for these same conditions. Recurrent disease is included for the following conditions: cancers, myocardial infarction, and various forms of strokes. A detailed account of outpatient health services use, and data from the multiphasic health checkup, which was administered to each participant during the nine yearly follow-ups, are also included in the Master Records file. The labs and procedures included: chemistry, hematology, urinalysis, bacteriology, chest x-ray, GI x-ray, ultrasound, CT/MRI, mammogram, resting ECG, treadmill ECG, echocardiograms, nuclear scans, outpatient breast biopsy, cystoscopy, and cataract surgery. Inpatient utilization includes all hospitalizations, procedures done during a hospital stay, length of stay, admitting/discharge diagnosis. Part 2, Hospitalization, contains records of causes and dates of hospitalizations and discharges and nursing home admissions. There is also a section on incomplete reviews and the reasons for them. Demographic information and some lifestyle information from the multiphasic health checkup (e.g., smoking, alcohol, and Body Mass Index) are also in this file. Data Availability: These datasets have been documented extensively and are available from the ICPSR (Study No. 4219). * Dates of Study: 1971-1992 * Study Features: Longitudinal, Anthropometric Measures * Sample Size: ** 1971 cohort: 2,877 (baseline) ** 1980 cohort: 3,113 (baseline) ** 1971 & 1980: 5,990 ** Hospitalization: 14,730 Links: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04219 * HSRR: http://wwwcf.nlm.nih.gov/hsrr_search/view_hsrr_record_table.cfm?TITLE_ID=381&PROGRAM_CAME=toc_with_source2.cfm

Proper citation: Epidemiology of Chronic Disease in the Oldest Old (RRID:SCR_013466) Copy   

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http://www.census.gov/did/www/nlms/

A database based on a random sample of the noninstitutionalized population of the United States, developed for the purpose of studying the effects of demographic and socio-economic characteristics on differentials in mortality rates. It consists of data from 26 U.S. Current Population Surveys (CPS) cohorts, annual Social and Economic Supplements, and the 1980 Census cohort, combined with death certificate information to identify mortality status and cause of death covering the time interval, 1979 to 1998. The Current Population Surveys are March Supplements selected from the time period from March 1973 to March 1998. The NLMS routinely links geographical and demographic information from Census Bureau surveys and censuses to the NLMS database, and other available sources upon request. The Census Bureau and CMS have approved the linkage protocol and data acquisition is currently underway. The plan for the NLMS is to link information on mortality to the NLMS every two years from 1998 through 2006 with research on the resulting database to continue, at least, through 2009. The NLMS will continue to incorporate data from the yearly Annual Social and Economic Supplement into the study as the data become available. Based on the expected size of the Annual Social and Economic Supplements to be conducted, the expected number of deaths to be added to the NLMS through the updating process will increase the mortality content of the study to nearly 500,000 cases out of a total number of approximately 3.3 million records. This effort would also include expanding the NLMS population base by incorporating new March Supplement Current Population Survey data into the study as they become available. Linkages to the SEER and CMS datasets are also available. Data Availability: Due to the confidential nature of the data used in the NLMS, the public use dataset consists of a reduced number of CPS cohorts with a fixed follow-up period of five years. NIA does not make the data available directly. Research access to the entire NLMS database can be obtained through the NIA program contact listed. Interested investigators should email the NIA contact and send in a one page prospectus of the proposed project. NIA will approve projects based on their relevance to NIA/BSR''s areas of emphasis. Approved projects are then assigned to NLMS statisticians at the Census Bureau who work directly with the researcher to interface with the database. A modified version of the public use data files is available also through the Census restricted Data Centers. However, since the database is quite complex, many investigators have found that the most efficient way to access it is through the Census programmers. * Dates of Study: 1973-2009 * Study Features: Longitudinal * Sample Size: ~3.3 Million Link: *ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00134

Proper citation: National Longitudinal Mortality Study (RRID:SCR_008946) Copy   

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http://www.icpsr.umich.edu/icpsrweb/NACDA/studies/04076/version/1

A dataset of a survey of intergenerational relations among 2,044 adult members of some 300 three- (and later four-) generation California families: grandparents (then in their sixties), middle-aged parents (then in their early forties), grandchildren (then aged 16 to 26), and later the great-grandchildren as they turn age 16, and further surveys in 1985, 1988, 1991, 1994, 1997 and 2001. This first fully-elaborated generation-sequential design makes it possible to compare sets of parents and adult-children at the same age across different historical periods and addresses the following objectives: # To track life-course trajectories of family intergenerational solidarity and conflict over three decades of adulthood, and across successive generations of family members; # To identify how intergenerational solidarity, and conflict influence the well-being of family members throughout the adult life course and across successive generations; # To chart the effects of socio-historical change on families, intergenerational relationships, and individual life-course development during the past three decades; # To examine women''s roles and relationships in multigenerational families over 30 years of rapid change in the social trajectories of women''s lives. These data can extend understanding of the complex interplay among macro-social change, family functioning, and individual well-being over the adult life-course and across successive generations. Data Availability: Data from 1971-1997 are available through ICPSR as Study number 4076. * Dates of Study: 1971-2001 * Study Features: Longitudinal * Sample Size: ** 345 Three-generational families ** 2,044 Adults (1971 baseline) Link: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04076

Proper citation: Longitudinal Study of Generations (RRID:SCR_008939) Copy   

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

A follow-up of the 1976-1977 MFLS-1 dataset covering the respondents'' and spouses'' marriage, fertility, employment, education and migration histories as well as extensive information on the household economy. The MFLS-2 contains a supplementary sample of persons age 50 or older. The data permit analysis of intergenerational transfers to the elderly and their covariates; the living arrangements of the elderly; the health of the elderly; labor supply, occupation and retirement status of the elderly; and their migration patterns. This supplement fills the gap left by many standard sources of demographic and economic information about Third World populations, such as fertility surveys and labor force surveys, which effectively exclude the elderly. Field work for MFLS-2 began in Aug. 1988 and was completed in Jan. 1989. The survey was fielded in four samples: * The Panel Sample Women who were the primary respondents to the MFLS-1, who at that time (1976) were ever-married women aged 50 or younger. There are 926 panel households in MFLS-2, a follow-up rate of 72%. * The Children Sample Children aged 18 or older in 1988 of the women interviewed as primary respondents for MFLS-1; i.e. adult children of the women eligible for the MFLS-2 Panel sample. There were interviews with one child, selected at random, inside the Panel household and two children, selected at random, living elsewhere in Peninsular Malaysia. There are 1,136 respondents in the Children sample. * The New Sample A sample of households with a woman aged 18-49 (regardless of her marital status) or an ever-married woman under age 18. There are 2,184 respondents in MFLS-2 New Sample. * The Senior Sample Selected households with a person age 50 or over. There are 1,357 respondents in the Senior Sample. Data Availability: The MFLS-2 (and MFLS-1) data files and documentation are available on-line or from NACDA at ICPSR as Study No. 9805. * Dates of Study: 1988-1989 * Study Features: International * Sample Size: Seniors (aged 50+): 1,357 Link: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/09805

Proper citation: Second Malaysian Family Life Survey (RRID:SCR_008892) Copy   

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