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4,694 results for “data analysis”
Data from: Diversification dynamics of Cheilostome Bryozoa based on a Bayesian analysis of the fossil record
<p>Cheilostomata is the most diverse and ecologically dominant order of bryozoans living today. We apply a Bayesian framework to estimate macroevolutionary rates of cheilostomes since the Late Jurassic across four datasets: I) manually curated genus ranges, II) published text-mined genus ranges, III) non-revised Paleobiology Database (PBDB) records, IV) revised and augmented PBDB records. All datasets revealed increased origination rates in the Albian, and a twin K-Pg and Danian extinction rate peak. High origination rates in the late Selandian-Ypresian in Dataset I indicate the onset of an ascophoran-grade radiation. Lineage-through-time plots confirm the macroevolutionary lag preceding the radiation of cheilostomes in the mid-Cretaceous, and their renewed diversification in the late Paleocene and Eocene. A multivariate birth-death model indicates that origination rates are shaped by diversity-dependent dynamics coupled with a positive correlation with sea surface temperature, while extinction rates negatively correlate with sea level. Text-mined data provide broadly similar rate dynamics as manually curated data, although discrepancies could be attributed to the omission of key literature in Dataset II, and the inclusion of new published and unpublished data, and revised ranges in Dataset I. Revision and augmentation of PBDB occurrences were necessary to generate rate profiles akin to those of Datasets I and II and highlight the risks of using unedited occurrence data. Our results support the widely held assumption that diversification dynamics are controlled by both biotic and abiotic factors and pave the way for integrating fossils with molecular phylogenies to study these processes in more detail.</p>
Data for "Training data composition affects performance of protein structure analysis algorithms" by A. Derry, K. A. Carpenter, & R. B. Altman
<p><strong>Description</strong></p> <p>This repository contains all data used in "Training data composition affects performance of protein structure analysis algorithms", published in the Pacific Symposium on Biocomputing 2022 by A. Derry, K. A. Carpenter, & R. B. Altman. </p> <p>The data consists of the following files:</p> <ul> <li>ema_zenodo_data.tar.gz: train, validation, and test splits for Estimation of Model Accuracy task, in LMDB format</li> <li>design_zenodo_data.tar.gz: train, validation, and test splits for Protein Sequence Design task, in JSON format</li> <li>enz_cat_res_zenodo_data.tar.gz: train, validation, and test splits for Catalytic Residue and Enzyme Prediction task, in TF record format</li> </ul> <p>Details on dataset construction can be found in our paper and dataloaders can be found in our <a href="https://github.com/awfderry/ml-structure-bias">Github repo</a>.</p> <p><strong>Reference</strong></p> <p>A. Derry*, K. A. Carpenter*, & R. B. Altman, "Training data composition affects performance of protein structure analysis algorithms", 2021.</p> <p><strong>Dataset References</strong></p> <p>Datasets used were derived from the following works:</p> <p>Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2019). Critical assessment of methods of protein structure prediction (CASP)—Round XIII. In <em>Proteins: Structure, Function and Bioinformatics</em> (Vol. 87, Issue 12, pp. 1011–1020). https://doi.org/10.1002/prot.25823</p> <p>Ingraham, J., Garg, V. K., Barzilay, R., & Jaakkola, T. (2019). <em>Generative Models for Graph-Based Protein Design</em>. https://openreview.net/pdf?id=SJgxrLLKOE</p> <p>Furnham, N., Holliday, G. L., de Beer, T. A. P., Jacobsen, J. O. B., Pearson, W. R., & Thornton, J. M. (2014). The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. <em>Nucleic Acids Research</em>, <em>42 </em>(Database issue), D485–D489.</p>
2021 UN Open GIS Challenge 1 - Training on Satellite Data Analysis and Machine Learning with QGIS (Satellite_QGIS)
<p>This dataset is part of the <a href="https://www.osgeo.org/foundation-news/2021-osgeo-un-committee-educational-challenge/?fbclid=IwAR0UvwkPO2pay7C0tJawb63eewjBGfeL9TIQpYUFccza9OIo6HAolmHXLWE">2021 UN Open GIS Challenge 1 - Training on Satellite Data Analysis and Machine Learning with QGIS (Satellite_QGIS)</a>,</p> <p>Exercise 1: Supervised Change Detection: Monitoring deglaciation in Huascaran, Peru.</p>
Data for: Analysis of Conformational Exchange Processes using Methyl-TROSY-Based Hahn Echo Measurements of Quadruple-Quantum Relaxation
<p>Raw experimental data used in associated publication. A full list of experiments is provided in the README.md file.</p>
Spatiotemporal analysis of plankton drivers in the Belgian part of the North Sea. Data, scripts and model output
This archive contains the input data, R scripts and final results of a mechanistic model that uses near real-time data from the Belgian Part of the North Sea (2011-2017) to quantify the relative contributions of the bottom-up and top-down drivers in phytoplankton dynamics. Input data are zooplankton and phytoplankton abundances, nutrients, Sea Surface Temperature (SST), photosynthetically active radiation (PAR); from the LifeWatch data and infrastructure, funded by Research Foundation - Flanders (FWO). Water temperature data for one of the locations was obtained from Flemish Banks Monitoring Network at https://meetnetvlaamsebanken.be/. The R scripts are presented in a R Markdown file that can be executed in the Blue-Cloud Zoo and Phytoplankton EOV products Vlab at https://blue-cloud.d4science.org/web/zoo-phytoplankton_eov, operated by D4Science.org, www.d4science.org (Assante et al., 2019).
CaImAn: An open source tool for scalable Calcium Imaging data Analysis
<p>Advances in fluorescence microscopy enable monitoring larger brain areas <em>in-vivo</em> with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. We present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to preprocessing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good scalability on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data.</p> <p>To benchmark the performance of CaImAn we collected and combined a corpus of manual annotations from multiple labelers on nine mouse two-photon datasets, that are contained in this open access repository. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.</p> <p>In order to reproduce the results of the paper or download the annotations and the raw movies, please refer to the readme.md at:</p> <p>https://github.com/flatironinstitute/CaImAn/blob/master/use_cases/eLife_scripts/README.md</p> <p> </p>
Towards a Data-Driven Requirements Engineering Approach: Automatic Analysis of User Reviews
<p>6000 French user reviews from three applications on Google Play (Garmin Connect, Huawei Health, Samsung Health) are labelled manually. We selected four labels: rating, bug report, feature request and user experience.</p> <ul> <li><strong>Ratings</strong> are simple text which express the overall evaluation to that app, including praise, criticism, or dissuasion.</li> <li><strong>Bug reports</strong> show the problems that users have met while using the app, like loss of data, crash of app, connection error, etc.</li> <li><strong>Feature requests</strong> reflect the demande of users on new function, new content, new interface, etc.</li> <li>In <strong>user experience</strong>, users describe their experience in relation to the functionality of the app, how does certain functions be helpful.</li> </ul> <p>As we can observe from the following table, that shows examples of labelled user reviews, each review belongs to one or more categories.</p> <table> <tbody> <tr> <th>App</th> <th>Total</th> <th>Rating</th> <th>Bug report</th> <th>Feature request</th> <th>User experience</th> </tr> </tbody> <tbody> <tr> <td>Garmin Connect</td> <td>2000</td> <td>1260</td> <td>757</td> <td>170</td> <td>493</td> </tr> <tr> <td>Huawei Health</td> <td>2000</td> <td>1068</td> <td>819</td> <td>384</td> <td>289</td> </tr> <tr> <td>Samsung Health</td> <td>2000</td> <td>1324</td> <td>491</td> <td>486</td> <td>349</td> </tr> </tbody> </table> <p> </p> <h2>New Dataset</h2> <p>Based on this dataset, we developed a labeled dataset containing 6,000 English and 6,000 French reviews for classification, as well as 1,200 bilingual reviews for clustering. The new dataset has been made publicly available on Zenodo at the following link: <a href="../records/11066414">https://zenodo.org/records/11066414</a></p>
BIO4AFRICA_Survey Data Uganda - Analysis of the needs and contexts of target farmers and rural communities with a gender lens_D1.1_311022_1
<p>The results of this survey support the identification of the needs, challenges, and context of target farmers and rural communities and how, why and under which circumstances the social, economic, regulatory, institutional, market and political circumstances could act as a barrier or an enabler for the uptake of bio-based solutions.</p>
BIO4AFRICA_Survey Data Senegal - Analysis of the needs and contexts of target farmers and rural communities with a gender lens_D1.1_101022_1
<p>The results of this survey support the identification of the needs, challenges, and context of target farmers and rural communities and how, why and under which circumstances the social, economic, regulatory, institutional, market and political circumstances could act as a barrier or an enabler for the uptake of bio-based solutions.</p>
BIO4AFRICA_Survey Data Ghana - Analysis of the needs and contexts of target farmers and rural communities with a gender lens_D1.1_101022_1
<p>The results of this survey support the identification of the needs, challenges, and context of target farmers and rural communities and how, why and under which circumstances the social, economic, regulatory, institutional, market and political circumstances could act as a barrier or an enabler for the uptake of bio-based solutions.</p>
BIO4AFRICA_Survey Data Ivory Coast - Analysis of the needs and contexts of target farmers and rural communities with a gender lens_D1.1_311022_1
<p>The results of this survey support the identification of the needs, challenges, and context of target farmers and rural communities and how, why and under which circumstances the social, economic, regulatory, institutional, market and political circumstances could act as a barrier or an enabler for the uptake of bio-based solutions.</p>
Data for: Resetting our expectations for parasites and their effects on species interactions: A meta-analysis
<p>Despite the ubiquitous nature of parasitism, how parasitism alters the outcome of host species interactions such as competition, mutualism, and predation remain unknown. Using a phylogenetically informed meta-analysis of 154 studies, we examined how the mean and variance in the outcomes of species interactions differed between parasitized and non-parasitized hosts. Overall, parasitism did not significantly affect the mean or variance of host species interaction outcomes, nor did the shared evolutionary histories of hosts and parasites have an effect. Instead, there was considerable variation in outcomes, ranging from strongly detrimental to strongly beneficial for infected hosts. Trophically-transmitted parasites increased the negative effects of predation, parasites increased and decreased the negative effects of interspecific competition for parasitized and non-parasitized heterospecifics, respectively, and parasites had particularly strong negative effects on host species interactions in freshwater and marine habitats, yet were beneficial in terrestrial environments. Our results illuminate the diverse ways in which parasites modify critical linkages in ecological networks, implying that whether the cumulative effects of parasitism are considered detrimental depends not only on the interactions between hosts and their parasites, but also on the many other interactions that hosts experience.</p>
Data from: Which traits optimize plant benefits? Meta-analysis on the effect of partner traits on the outcome of an ant-plant protective mutualism
<p><span>1. Theoretical models on mutualism dynamics predict that partner traits may influence the outcome of mutualistic interactions. However, most empirical data on this issue is restricted to case studies, limiting our ability to reach a more widespread comprehension of the role of partner traits on the dynamic of mutualisms. </span></p> <p><span>2. We investigated how the outcome of protective mutualisms between ants and plants bearing extrafloral nectaries (EFNs) is influenced by the traits of EFNs and ants feeding on EFNs. We used a meta-analytical approach based on 35 studies investigating the effect of ant attendance on the herbivores and reproductive performance of EFN-bearing plants. We evaluated how variation in the EFN vascularization and location on plants and the ant aggressiveness can modulate the effect of ant attendance on the plants. </span></p> <p><span>3. Both plant and ant traits investigated here drove the outcome of the protective mutualism for EFN-bearing plants. Plants exclusively bearing EFNs near reproductive organs benefited more from ant attendance than plants bearing EFNs on vegetative or vegetative and reproductive organs. Ants had a higher positive impact on the reproductive performance of plants bearing non-vascularized EFNs than plants bearing vascularized EFNs, although their effects on herbivores had been similar in both plant types. Regarding the ant behavior, plants often attended by more aggressive ant species had a higher reproductive performance than plants often attended by less aggressive ones. </span></p> <p><span>4. Synthesis</span><span>: Our results highlight that the selective pressures and evolutionary routes in ant-plant protective mutualisms may depend on the pool of traits exhibited by partner species. Although some studies have already reported some impact of species traits on the outcome of ant-plant mutualisms, this is the first time that a generalization about the role of species traits on the net balance of ant attendance was proposed. Due to this generalization, it was possible to advance our knowledge about the evolution of facultative mutualisms by showing that the role of species traits on the mutualistic outcome can vary in intricate ways due to a particular trait combination found among partners in communities where the interactions are embedded in.</span></p>
Data and Analysis of Reading and Assessment Activities in Moodle
<p><strong>Interactions of reading and assessment activities in Moodle</strong></p> <p>Reading and assessment are elementary activities for knowledge acquisition in online learning. Assessments represented as quizzes can help learners to identify gaps in their knowledge and understanding, which they can then overcome by reading the corresponding text-based course material. Reversely, quizzes can be used to evaluate reading comprehension. In this paper, we ex- amine the interactions between reading and quiz activities using scroll and log data from an online undergraduate course (N=142). By analyzing processes and sequential patterns in user sessions, we identified six session clusters for characteristic reading and quiz patterns potentially relevant for adaptive learning support. Using these session clusters, we further clustered students by their reading and quiz behavior over six time periods within the semester. The results hypothesize a personalization for seven groups of learners characterized by their temporal activity and predominant quiz and reading behavior.</p> <p> </p> <p><strong>Pre-requisites and install instructions</strong></p> <p>1. Make sure Python v3.9 is installed on your system.</p> <p>2. conda env create -f environment.yml</p> <p>3. conda activate analysis</p> <p>4. To replicate the analysis open the file Ananlysis.ipynb and execute the code blocks one by one or all together.</p> <p> </p> <p>`jupyter nbconvert --to python Analysis.ipynb`</p> <p>`jupyter notebook Analysis.py`</p> <p> </p> <p><strong>Files and folders</strong></p> <ul> <li>(File) Analysis.ipynb: Python Notebook containing all applied code blocks applied for data analysis.</li> <li>(File) requirements.txt: List of python modules to be installed to fulfill the requirements of the Analysis.ipynb script.</li> <li>(Folder) data: The folder contains anonymized CSV files for each Moodle database table that was necessary for the data analysis. All data files are text files encoded in UTF-8. The columns are separated with a semicolon (";"), and rows are indicated by line breaks ("\n"). <ul> <li>m_assign.csv: ...</li> <li>m_course_modules.csv: ...</li> <li>m_quiz.csv: ...</li> <li>no_students.csv: ...</li> <li>user_acceptances.csv: ...</li> <li>m_assign_grades.csv: ...</li> <li>m_course_sections.csv: ...</li> <li>m_quiz_attempts.csv: ...</li> <li>scroll.csv: ...</li> </ul> </li> </ul> <p> </p> <p><strong>Publications and citation</strong></p> <p><strong>Publications</strong></p> <ul> <li>Seidel, N., & Menze, D. (2022). Interactions of reading and assessment activities. In S. Sosnovsky, P. Brusilovsky, & A. Lan (Eds.), 4th Workshop on Intelligent Textbooks, 2022 (pp. 64–76). CEUR-WS. http://ceur-ws.org/Vol-3192/</li> <li>Menze, D., Seidel, Ni., & Kasakowskij, R. (2022). Interaction of reading and assessment behavior. In P. A. Henning, M. Striewe, & M. Wölfel (Eds.), DELFI 2022 – Die 21. Fachtagung Bildungstechnologien der Gesellschaft für Informatik e.V. (pp. 27–38). Gesellschaft für Informatik. https://doi.org/10.18420/delfi2022-011</li> </ul> <p><strong>Citation of the dataset</strong></p> <ul> <li>Seidel, Niels, & Menze, Dennis. (2022). Data and Analysis of Reading and Assessment Activities in Moodle (1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.730007</li> </ul> <p>The source code and data are maintained at GitHub: <a href="https://github.com/nise/delfi22">https://github.com/nise/delfi22</a></p> <p> </p> <p><strong>Acknowledgments </strong>This research was supported by <em>CATALPA - Center of Advanced Technology for Assisted Learning and Predictive Analytics</em> of the FernUniversität in Hagen, Germany.</p>
Supplemental Data and Code for "An exact version of Life Table Response Experiment analysis, and the R package exactLTRE"
<p>This dataset enables the user to repeat the analyses presented in the manuscript "An exact version of Life Table Response Experiment analysis, and the R package exactLTRE." It is comprised of two compressed archives: one which contains code, and one which contains data.</p>
Data for: Multi-omics analysis identifies symbionts and pathogens of blacklegged ticks (Ixodes scapularis) from a Lyme disease hotspot in southeastern Ontario, Canada
<p>Ticks in the family Ixodidae are recognized as important vectors of zoonoses including Lyme disease (LD), which is caused by spirochete bacteria from the <em>Borreliella</em> (<em>Borrelia</em>) <em>burgdorferi</em> sensu lato (<em>Bbsl</em>) complex. The blacklegged tick (<em>Ixodes scapulars</em>) continues to expand across Canada, creating hotspots of elevated LD risk at the leading edge of its expansion range. Current efforts to understand the risk of pathogen transmission associated with <em>I. scapularis</em> in Canada focus primarily on targeted screens, while variation in the tick microbiome remains poorly understood. Using multi-omics consisting of 16S metabarcoding and ribosome-depleted, whole-shotgun RNA transcriptome sequencing, we examined the microbial communities associated with adult <em>I. scapularis</em> (N = 32), sampled from four tissue types (whole tick, salivary glands, midgut, and viscera) and three geographical locations within an LD hotspot near Kingston, Ontario. The communities consisted of both endosymbiotic and known or potentially pathogenic microbes, including RNA viruses, bacteria, and a <em>Babesia</em> sp. intracellular parasite. We show that β-diversity is significantly higher between individual tick salivary gland and midgut bacterial communities, compared to whole ticks; while linear discriminant analysis (LDA) effect size (LEfSe) determined that the three potentially pathogenic bacteria detected by V4 16S rDNA sequencing were also discriminatory for dissected tissues only, including a <em>Borrelia</em> from the <em>Bbsl</em> complex, <em>Borrelia miyamotoi</em>, and <em>Anaplasma phagocytophilum. </em>Importantly, we find co-infection of <em>I. scapularis</em> by multiple microbes, in contrast to diagnostic protocols for LD, which typically focus on infection from a single pathogen of interest (<em>B. burgdorferi</em> sensu stricto).</p>
The data sheet of "Phytochemicals, Proximate Composition, Minerals and Volatile Oil Analysis of Zanthoxylum acanthopodium DC. Fruits"
<p>The dataset of ‘Phytochemicals, Proximate Composition, Minerals and Volatile Oil Analysis of <em>Zanthoxylum acanthopodium</em> DC. Fruits’</p>
Digital Twins: A Systematic Literature Review Based on Data Analysis and Topic Modeling
<p>The digital twin has recently become a popular topic in research related to manufacturing, such as Industry 4.0, the industrial internet of things, and cyber-physical systems. In addition, digital twins are the focus of several research areas: construction, urban management, digital transformation of the economy, medicine, virtual reality, software testing, and others. The concept is not yet fully defined, its scope seems unlimited, and the topic is relatively new; all this can present a barrier to research. The main goal of this paper is to develop a proper methodology for visualizing the digital-twin science landscape using modern bibliometric tools, text-mining and topic-modelling, based on machine learning models—Latent Dirichlet Allocation (LDA) and BERTopic (Bidirectional Encoder Representations from Transformers). The scope of the study includes 8693 publications on the topic selected from the Scopus database, published between January 1993 and September 2022. Keyword co-occurrence analysis and topic-modelling indicate that studies on digital twins are still in the early stage of development. At the same time, the core of the topic is growing, and some topic clusters are emerging. More than 100 topics can be identified; the most popular and fastest-growing topic is ‘digital twins of industrial robots, production lines and objects.’ Further efforts are needed to verify the proposed methodology, which can be achieved by analyzing other research fields.</p>
Extended data: Tissue-specific multi-omics analysis of atrial fibrillation
<p>Summary statistics and result repository for the publication Tissue-specific multi-omics analysis of atrial fibrillation:</p> <p>Assum, I., Krause, J., Scheinhardt, M.O. <em>et al.</em> Tissue-specific multi-omics analysis of atrial fibrillation. <em>Nat Commun </em><strong>13, </strong>441 (2022). https://doi.org/10.1038/s41467-022-27953-1</p> <p>For the related source code, see https://doi.org/https://doi.org/10.5281/zenodo.5094276 or https://github.com/heiniglab/symatrial.</p> <p>Ines Assum<sup>1,2,†</sup>, Julia Krause<sup>3,4,†</sup>, Markus O. Scheinhardt<sup>5</sup>, Christian Müller<sup>3,4</sup>, Elke Hammer<sup>6,7</sup>, Christin S. Börschel<sup>4,8</sup>, Uwe Vöker<sup>6,7</sup>, Lenard Conradi<sup>9</sup>, Bastiaan Geelhoed<sup>4,8,10</sup>, Tanja Zeller<sup>3,4,</sup>*, Renate B. Schnabel<sup>4,8,</sup>*, Matthias Heinig<sup>1,2,11,</sup>*</p> <p><sup>† </sup>,* These authors contributed equally.</p> <p><sup> 1</sup> Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.<br> <sup> 2</sup> Department of Informatics, Technical University Munich, München, Germany.<br> <sup> 3</sup> University Center of Cardiovascular Science, University Heart and Vascular Center Hamburg, Hamburg, Germany.<br> <sup> 4</sup> Partner site Hamburg/Kiel/Lübeck, DZHK (German Center for Cardiovascular Research), Hamburg, Germany.<br> <sup> 5</sup> Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany.<br> <sup> 6</sup> Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.<br> <sup> 7</sup> Partner site Greifswald, DZHK (German Center for Cardiovascular Research), Greifswald, Germany.<br> <sup> 8</sup> Department of Cardiology, University Heart and Vascular Center Hamburg, Hamburg, Germany.<br> <sup> 9</sup> Department of Cardiovascular Surgery, University Heart and Vascular Center Hamburg, Hamburg, Germany.<br> <sup>10 </sup>Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.<br> <sup>11</sup>Partner site Munich, DZHK (German Center for Cardiovascular Research), Munich, Germany.</p> <p> </p> <p>ABSTRACT:</p> <p>Genome-wide association studies (GWAS) for atrial fibrillation (AF) have uncovered numerous disease-associated variants. Their underlying molecular mechanisms, especially consequences for mRNA and protein expression remain largely elusive. Thus, refined multi-omics approaches are needed for deciphering the underlying molecular networks. Here, we integrate genomics, transcriptomics, and proteomics of human atrial tissue in a cross-sectional study to identify widespread effects of genetic variants on both transcript (cis-eQTL) and protein (cis-pQTL) abundance. We further establish a novel targeted transQTL approach based on polygenic risk scores to determine candidates for AF core genes. Using this approach, we identify two trans-eQTLs and five trans-pQTLs for AF GWAS hits, and elucidate the role of the transcription factor NKX2-5 as a link between the GWAS SNP rs9481842 and AF. Altogether, we present an integrative multi-omics method to uncover trans-acting networks in small datasets and provide a rich resource of atrial tissue-specific regulatory variants for transcript and protein levels for cardiovascular disease gene prioritization.</p> <p>This version contains a reference file identifying effect alleles for all QTL results and adds additional genotype and allele frequency information for all QTL SNPs. </p> <p>TABLE OF CONTENTS:</p> <ul> <li>Reference for effect alleles<br> <em>map_AFHRI_B_effect_alleles.txt</em></li> <li>Reference for genotype and allele frequencies (derived using PLINK) <ul> <li><em>genotype_allele_frequencies_eQTL_SNPs.txt</em></li> <li><em>genotype_allele_frequencies_pQTL_SNPs.txt</em></li> <li><em>genotype_allele_frequencies_resQTL_SNPs.txt</em></li> </ul> </li> <li>Single-omic <em>cis</em>-QTL results <ul> <li><em>cis</em>-eQTLs (all pairs, incl. LD clump info)<br> <em>eQTL_right_atrial_appendage_allpairs_clump.txt</em></li> <li><em>cis</em>-pQTLs (all pairs, incl. LD clump info)<br> <em>pQTL_right_atrial_appendage_allpairs_clump.txt</em></li> <li><em>cis</em>-res eQTLs (all pairs, incl. LD clump info)<br> <em>res_eQTL_right_atrial_appendage_allpairs_clump.txt</em></li> <li><em>cis</em>-res pQTLs (all pairs, incl. LD clump info)<br> <em>res_pQTL_right_atrial_appendage_allpairs_clump.txt</em></li> <li><em>cis</em>-ratioQTLs (all pairs, incl. LD clump info)<br> <em>ratioQTL_right_atrial_appendage_allpairs_clump.txt</em></li> </ul> </li> <li>Functional <em>cis</em>-QTL categories and eQTL/pQTL overlap: <ul> <li>All eQTLs, pQTLs, res eQTLs, res pQTLs and ratioQTLs for all SNP-gene pairs with a significant eQTL and pQTL (FDR<0.05)<br> <em>Fig2a_source_data_Shared_eQTL_pQTL_clump.txt</em></li> <li>All eQTLs, pQTLs, res eQTLs, res pQTLs and ratioQTLs for all SNP-gene pairs with a significant eQTL but no pQTL (FDR<0.05)<br> <em>Fig2b_source_data_Independent_eQTL_clump.txt</em></li> <li>All eQTLs, pQTLs, res eQTLs, res pQTLs and ratioQTLs for all SNP-gene pairs with no eQTL but a significant pQTL (FDR<0.05)<br> <em>Fig2c_source_data_Independent_pQTL_clump.txt</em><span> </span></li> </ul> </li> <li>QTS rankings and enrichment results <ul> <li>eQTS rankings and enrichments<br> <em>TableS6_source_data_eQTS_ranking.txt<br> TableS7_source_data_eQTS_GSEA_results.txt</em></li> <li>pQTS rankings and enrichments<br> <em>TableS8_source_data_pQTS_ranking.txt<br> TableS9_source_data_pQTS_GSEA_results.txt</em></li> </ul> </li> <li><em>Trans</em>-QTLs<br> all tested pairs including <em>trans</em>-pQTLs for <em>trans</em>-eQTLs and <em>trans</em>-eQTLs for <em>trans</em>-pQTLs<br> <em>Table2_source_data_Trans-QTL_results.txt</em></li> </ul> <p> </p>
Data and code for reproducing analysis in 'Producing indicative allocations for Community Led Local Development funding in Scotland (2022-23)'
<p>The data and code in this folder can be used to reproduce work used to generate indicative allocations of Community Led Local Development funding (2022-23) to 21 Local Action Group (LAG) areas in Scotland. It accompanies a note ('Producing indicative allocations for Community Led Local Development funding in Scotland (2022-23)', <a href="https://doi.org/10.5281/zenodo.7418862">https://doi.org/10.5281/zenodo.7418862</a>) providing an overview of the analysis and its key outputs.</p>
ScienceDex guides
Understand access before you commit
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.