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376 results for “Causality”
Processed data from "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"
<p>This is the processed data from our manscript "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"</p>
Processed data from "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"
<p>This is the processed data from our manscript "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"</p>
Processed data from "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"
<p>This is the processed data from our manscript "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"</p>
Data and code for "Large language models identify causal genes in complex trait GWAS"
<p><span>This file contains the data and scripts for the preprint "Large language models identify causal genes in complex trait GWAS"</span></p>
Kinex infers causal kinases from phosphoproteomics data
<p>Reference table of 82,755 pre-scored peptides containing serine and/or threonine phosphorylation sites for 303 kinases. This reference table is used as input for Kinex, a Python package, which infers causal serine/threonine kinases from phosphoproteomics data. <br><br>Kinex is released with the GNU General Public License, openly accessible to all users at https://github.com/bedapub/kinex.</p>
The Impact of the #MeToo Movement on Language at Court - A text-based causal inference approach
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MoCA causal model V1.0
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Data and code for Causality analysis and prediction of riverine algal blooms by combining empirical dynamic modeling and machine learning techniques
<p>Hydrological data (including daily water levels, flow velocities, and streamflow discharges) from two hydrological stations, the Hankou Station in the Yangtze River (YR) and the Hanchuan Station in the Han River (HR), were obtained from Hubei Province Hydrology and Water Resources Center.</p> <p>Water quality data (i.e., total nitrogen (TOTN), total phosphorus (TOTP), and water temperature in the Han River) and algae densities at three sections (Baihezui, Qinduankou and Zongguan) were acquired from the Yangtze River Basin Ecological and Environmental Supervision Authority. </p> <p><span>The R script(s) for machine learning models can also be found at <a href="../api/records/10901736/draft/files/Code%20for%20machine%20learning%20classification%20model.R/content" target="_blank" rel="noopener noreferrer">Code for machine learning classification model.R</a>.</span></p> <p> </p>
Causality Inference Datasets
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NOX5-induced uncoupling of endothelial NO synthase is a causal mechanism and theragnostic target of an age-related hypertension endotype
<p></p><p>Hypertension is the most important cause of death and disability in the elderly. In 9 out of 10 cases, the molecular cause, however, is unknown. One mechanistic hypothesis involves impaired endothelium-dependent vasodilation through reactive oxygen species (ROS) formation. Indeed, ROS forming NADPH oxidase (Nox) genes associate with hypertension, yet target validation has been negative. We re-investigate this association by molecular network analysis and identify NOX5, not present in rodents, as a sole neighbor to human vasodilatory endothelial nitric oxide (NO) signaling. In hypertensive patients, endothelial microparticles indeed contained higher levels of NOX5—but not NOX1, NOX2, or NOX4—with a bimodal distribution correlating with disease severity. Mechanistically, mice expressing human Nox5 in endothelial cells developed—upon aging—severe systolic hypertension and impaired endothelium-dependent vasodilation due to uncoupled NO synthase (NOS). We conclude that NOX5-induced uncoupling of endothelial NOS is a causal mechanism and theragnostic target of an age-related hypertension endotype. Nox5 knock-in (KI) mice represent the first mechanism-based animal model of hypertension.</p><p></p>
Complete workflow for the prediction of the secretome of Fusarium oxysporum f. sp. albedinis, the causal agent of palm dieback
<p>Custom scripts for mining the secretome of <em>Fusarium oxysporum</em> f. sp. <em>albedinis</em>, the causal agent of date palm dieback disease. </p>
Oil-gas prices and economic activity in selected European countries – evidence form time and frequency domain causality
<p>Data sets related with research: <strong>Oil-gas prices and economic activity in selected European countries – evidence form time and frequency domain causality</strong>. - file name: Data - Time Series - DEU, NOR, POL</p> <p>results of Breitung-Candelon test</p>
Data for the manuscript 'Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework'.
<p>This zip file contains the data downloaded from external sources used to produce the results in the manuscript 'Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework'. Note that all of the data contained in this zip file was publicly available at the time of writing.</p> <p>The corresponding Github can be found here:<br> https://github.com/alan-turing-institute/jbc-turing-rss-testdebiasing</p> <p>The publication is available here:<br> https://doi.org/10.1038/s41564-021-01029-0</p>
Inferring causal cell-cell communication from single-cell transcriptomics
<p>Data used to produce the analysis in "Inferring causal cell-cell communication from single-cell transcriptomics" by Almet and Nie (2022)</p>
Causal effect of familial short stature on three quantitative traits in Taiwan
<p><span><strong>Objectives</strong>: </span><span>With the accumulation of genetic basis for </span><span>familial (genetic) short stature (FSS)</span><span>, the genetic association of FSS with health-related outcomes remains to be elucidated. In this study, we aimed to investigate the FSS genetic architecture and its causal effect on three quantitative traits in Taiwan. </span></p> <p><span><strong>Methods</strong>:</span><span> We </span><span>conducted an FSS genome-wide association study (GWAS) analysis (1,640 FSS cases and 22,372 controls). We performed a GWAS meta-analysis for the Taiwanese meta-height from the Taiwan Biobank (</span><span>TWB)_height (N = 67,452) and the China Medical University Hospital (CMUH)_height GWAS summary statistics (N = 88,854). </span><span>We calculated three polygenic risk scores (PRSs) of SNPs (<em>P</em> < 5 x 10<sup>-8</sup>) for FSS and Taiwanese meta-height with/without FSS, respectively. We explored the associations between three PRSs and the measured height, respectively. We also performed </span><span>Mendelian randomization (MR) analysis</span><span> for the causal effect of FSS and Taiwanese meta-height with/without FSS, on anthropometric, bone mineral density (BMD), and female reproductive traits</span><span>. </span></p> <p><span><strong>Results</strong>: </span><span>FSS GWAS identified 172 SNPs in 4 genomic regions, reported in height </span><span>(<em>P</em> < 5 x 10<sup>-8</sup>)</span><span>. Higher FSS genetic scores correlate with an increased risk of short stature and height reduction tendency </span><span>(</span><em><span>p</span></em> <span><</span><span> 0.001).</span><span> The causal effect showed that a higher risk of FSS was associated with decreased body height, but increased body mass index, and body fat</span> <span>(</span><em><span>p</span></em> <span><</span><span> 0.001)</span><span>. However, higher genetic scores of Taiwanese meta-height with/without FSS correspond with increased body height, body weight, hip circumference, and age at menarche, but decreased BMD_T-score, BMD_Z-score, and stiffness index </span><span>(</span><em><span>p</span></em> <span><</span><span> 0.001)</span><span>. </span></p> <p><span><strong>Conclusion</strong>: </span><span>This study </span><span>contributes to the FSS and height genetic features and their causal effects on three quantitative traits </span><span>in individuals of Han Chinese ancestry in Taiwan. </span></p>
Data from: Inferring causalities in landscape genetics: An extension of Wright's causal modeling to distance matrices
<p>Data files from Inferring causalities in landscape genetics: An extension of Wright's causal modeling to distance matrices.</p>
Time series used in the manuscript "Causal dependences between the coupled ocean-atmosphere dynamics over the Tropical Pacific, the North Pacific and the North Atlantic"
<p>These 6 files contain time series built using reanalyses datasets of the ECMWF as discussed in the manuscript "Causal dependences between the coupled ocean-atmosphere dynamics over the Tropical Pacific, the North Pacific and the North Atlantic" submitted for discussion in the journal "Earth System Dynamics".</p>
A Directed Acyclic Graph of causal relations between diseases mined from the literature
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Unravelling molecular signatures and causal factors underlying latent Cytomegalovirus infection among people living with HIV
<p>CMV seropositivity does not lead to severe <span>pathology </span>in healthy individuals, but it contributes to medical complications in people living with HIV (PLHIV). This study provides a comprehensive evaluation of how CMV <span>seropositivity</span> shapes the immune system of 1887 PLHIV, by utilizing multi-omics and deep immune phenotyping dataset<span>s</span>. We observed prominent CMV-induced signatures at the DNA methylome and transcriptome levels <span>that were </span>related to immune functions in PLHIV. High FCRL6 expression is a promising biomarker for immune activation in latent CMV infection, underlied by the demethylation of FCRL6 and up-regulation of gene expression and plasma protein concentrations in CMV<span>-seropositive</span><span> </span>PLHIV. Furthermore, the host genetics-driven elevation in both gene and protein expression of FCRL6 was associated with latent CMV infection. We also identified a significant CMV-susceptibility locus associated with cytokine production capacity and protein abundance.</p>
SynDrep: The causal-only pharmacome with drug-drug relations.
<p>The data to load the causal-only pharmacome adapted for the Human Brain Pharmacome and enriched with drug-drug relations (averaged form databses such as DrugcombDB, DrugcombPortal, and SYNERGxDB or predicted through the random forest classification of drug combinations, based on HolE embeddings).</p> <p>The data can be loaded into neo4j instances using the command in Command.txt file</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.