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466 results for “code analysis”
Application of Mass Multivariate Analysis on Neuroimaging Data Sets for Precision Diagnosis of Depression: Data and code
<p><strong>In the archive are the datasets and code used to create the results in article "Application of Mass Multivariate Analysis on Neuroimaging Data Sets fo Precision Diagnosis of Depression". The methods is based on the Multivariate Linear toolbox mad F. Kherif’s lab and available on GitHub. <a href="https://github.com/LREN-CHUV/MLM">https://github.com/LREN-CHUV/MLM</a>. </strong></p> <p><strong>A total of 44 patients with a current psychotic (n=19) or depressive (n=25) episode were analyzed by MLM (details can be found in the article itself) utilizing resting sate fMRI, tasks fMRI, and anatomical T1w images. </strong></p> <p><strong>The data results are provided in MATLAB format, in a matrix called MLM.mat. The matrix includes the canonical variables for each of the three imaging modalities, chi-square statistics, and p-values for each brain region. Additionally, we provided a function MLM_plot_fun that allows mapping the statistics results to a canonical three-dimensional brain as per the article. </strong></p>
Dataset and R code: Effects of temperature and air pollution on emergency ambulance dispatches: a time series analysis in a medium-sized city in Germany
<p>Dataset and R script to replicate results in the manuscript "Effects of temperature and air pollution on emergency ambulance dispatches: a time series analysis in a medium-sized city in Germany", currently under review.</p>
Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction. Analysis Code, Numerical and Primary data.
<p>Uploaded under this Zenodo DOI is the following:</p> <p>1. the Analysis Code used for Flow Cytometry analysis in the paper, GO complex analysis (Figure 3) and Hit visualization (Figure 1, 2 S1, S4 Figs).</p> <p>2. The primary Flow Cytometry data from both the initial screen (ScreenFlowFCS) and validation experiments (ValidationFlowFCS) are included as .zip files.</p> <p>3. a .zip folder is uploaded that contains all the analysis code for the ChIP-Seq experiments. </p> <p>4. Excel worksheets that contain the numerical source data for all qPCR bar plots.</p>
R_JAGS code for estimation and analysis of species-area-relationship (SAR) parameters from NEON (National Ecological Observatory Network) data on plant surveys
<p><span>Invasive species science is heavily geared toward the invasive agent. </span>However, management to protect native species also requires a proactive approach focused on understanding the features affecting community vulnerability to invasion impacts<span>. </span><span>Vulnerability </span><span>is likely the result of </span><span>factors acting across spatial scales, from </span><span>local to regional, and it is the combined effects of these factors that will determine the magnitude of vulnerability.</span><span> We introduce an analytical framework that quantifies the scale-dependent impact of biological invasions from the shape of the native species-area-relationship (SAR). We leverage newly available, biogeographically extensive vegetation data from the US National Ecological Observatory Network to assess plant community vulnerability to invasion impact as a function of factors acting across scales. We analyzed more than 1000 SARs widely distributed across the USA along environmental gradients and under different levels of invasion. </span>Results show that a decrease in native richness is consistently associated with invasive species cover<span>, but it is only at relatively high levels of invasion that native richness is compromised. After accounting for variation in baseline ecosystem diversity, net primary productivity, and human modification, ecoregions that are colder and wetter seem to be most vulnerable to losses of native plant species at the local level, while warmer and wetter areas seem most susceptible at the landscape level. We also document how the combined effects of cross-scale factors result in a heterogenous spatial pattern of vulnerability. </span><span>This pattern </span><span>cannot be predicted by analyses at any single scale, underscoring the importance of accounting for factors acting across scales. Simultaneously assessing differences in vulnerability between distinct plant communities at local, landscape and regional scales provided outputs that can be used to inform policy and management aimed at reducing vulnerability to the impact of plant invasions.</span></p>
Codes and model output supporting Analysis of the Evolution of Parametric Drivers of High-End Sea-Level Hazards
<p>Codes and model output supporting Analysis of the Evolution of Parametric Drivers of High-End Sea-Level Hazards (Advances in Statistical Climatology, Meteorology and Oceanography, May 2022)</p>
Dataset, statistical analysis code, and supplementary material of juvenile ravens' responses towards acoustic cues of different social categories
<p>Social competence i.e., defined as the ability to adjust the expression of social behaviour to the available social information, is known to be influenced by early-life conditions. Brood size might be one of the factors determining such early conditions, particularly in species with extended parental care. We here tested in ravens, whether growing up in families of different sizes affects the chicks' responsiveness to social information. We experimentally manipulated the brood size of 20 captive raven families, creating either small or large families. Simulating dispersal, juveniles were separated from their parents and temporarily housed in one of two captive non-breeder groups. After five weeks of socialization, each raven was individually tested in a playback setting with food-associated calls from three social categories: sibling, familiar unrelated raven they were housed with, and unfamiliar unrelated raven from the other non-breeder aviary. We found that individuals reared in small families were more attentive than birds from large families, in particular towards the familiar unrelated peer. These results indicate that variation in family size during upbringing can affect how juvenile ravens value social information. Whether the observed attention patterns translate into behavioural preferences under daily life conditions remains to be tested in future studies.</p>
Data and analysis code for: Global protected areas seem insufficient to safeguard half of the world's mammals from human-induced extinction
<div> <p class="normal">Protected areas (PAs) are a cornerstone of global conservation and central to international plans to minimize global extinctions. During the coming century, global ecosystem destruction and fragmentation associated with increased human population and economic activity could make the <span class="PI"></span>long-term<span class="PI"></span> survival of most terrestrial vertebrates even more dependent on PAs. However, the capacity of the current global PA network to sustain species for the long term is unknown. Here, we explore this question for all <span class="PI"></span>nonvolant terrestrial mammals<span class="ins cts-1"> for which we found sufficient data</span>, ∼4,000 species. We first estimate the potential population size of each such mammal species in each PA and then use three different criteria to estimate if solely the current global network of PAs might be sufficient for their <span class="PI"></span>long-term<span class="PI"></span> survival. Our analyses suggest that current PAs may fail to provide robust protection for about half the species analyzed, including most species currently listed as threatened with extinction and a third of species not currently listed as threatened. Hundreds of mammal species appear to have no viable protected populations. Underprotected species were found across all body sizes, taxonomic groups, and geographic regions. <span class="PI"></span>Large-bodied<span class="PI"></span> mammals, endemic species, and those in <span class="PI"></span>high-biodiversity<span class="PI"></span> tropical regions were particularly poorly protected by existing PAs. As<span class="ins cts-1"> new</span> international biodiversity targets are formulated, our results suggest that the global network of PAs must be <span class="PI"></span>greatly expanded and most importantly that PAs must be located in diverse regions that encompass species not currently protected and must be large enough to ensure that protected species can persist for the long term.</p> </div> <p class="kwd-group"></p>
Excitation energy transfer and vibronic coherence in intact phycobilisomes — multidimensional electronic spectroscopy data set and MATLAB and Julia analysis code
<p>Data sets used in the article "Excitation energy transfer and vibronic coherence in intact phycobilisomes" by Sil et al. The phycobilisomes were isolated from the short-filament mutant (SF33) of <em>Fremyella diplosiphon</em> UTEX 481 (also known as <em>Tolypothrix</em> sp. PCC 7601). Multidimensional electronic spectroscopy was performed with 6.7 fs mid-visible pulses (520–700 nm) using a pump–probe optical configuration using adaptive pulse shaping techniques. In addition to the full set of two-dimensional spectra and analysis files generated using global and target modeling and analysis of coherences (3DES oscillation maps), we provide here a linear absorption spectrum with phycobiliprotein component analysis as well as a set of 2D excitation–emission fluorescence spectra of intact and broken phycobilisome preparations. </p> <p>Sil, S.; Tilluck, R. W.; Mohan TM, N.; Leslie, C. H.; Rose, J. B.; Domínguez-Martín, M. A.; Lou, W.; Kerfeld, C. A.; Beck, W. F. Excitation energy transfer and vibronic coherence in intact phycobilisomes. Nat. Chem. (2022), DOI: 10.1038/s41557-022-01026-8.</p> <p><a href="https://urldefense.com/v3/__https://www.nature.com/articles/s41557-022-01026-8__;!!HXCxUKc!yaVwTZFk8T-j3ROhygpOGW5Xy_E2wQvf-QgNGr9FZZbp4oNpfp_ZmhkdWYLdg2mKSDP8yYrNAZs$">https://www.nature.com/articles/s41557-022-01026-8</a></p> <p> </p> <p> </p>
QENS spectra of myoglobin in solution to be used with the analysis codes deposited under 10.5281/zenodo.7058345
<p>Quasielastic Neutron Scattering spectra of myoglobin in solution recorded on the IN5 spectrometer at the Institut Laue-Langevin in Grenoble, France. The data sets are to be used with the analysis codes deposited under DOI:10.5281/zenodo.7058345, which are in turn related to the publication A. Hassani, A. M. Stadler, and G.R. Kneller, Quasi-analytical resolution-correction of elastic neutron scattering from proteins, to appear in the Journal of Chemical Physics (DOI:10.1063/5.0103960). </p> <p>The data can be freely used, citing properly the reference concerning the original data, A. M. Stadler, F. Demmel, J. Ollivier, and T. Seydel, Picosecond to Nanosecond Dynamics Provide a Source of Conformational Entropy for Protein Folding. Phys. Chem. Chem. Phys., 18(31):21527–21538, 2016 (DOI: 10.1039/c6cp04146a).</p> <p> </p>
Sample 3D image data from RIMS method for image analysis code demo
<p>Sample 3D image data from RIMS method applied to mechanical test on hydrogel sphere packings, to be used in image analysis code demo as demonstrated in the ALERT Geomechanics doctoral school 2022. The data is a small subset from a larger set of data as found on Dryad via 10.5061/dryad.6djh9w0x8 and is separated here on Zenodo to make the subset more machine-readable.</p>
Data and code – Effects of climate on salmonid productivity: A global meta-analysis across freshwater ecosystems
<p>Salmonids are of immense socio-economic importance in much of the world but are threatened by climate change. This has generated a substantial literature documenting effects of climate variation on salmonid productivity in freshwater ecosystems, but there has been no global quantitative synthesis across studies. We conducted a systematic review and meta-analysis to gain quantitative insight into key factors shaping the effects of climate on salmonid productivity, ultimately collecting 1,321 correlations from 156 studies, representing 23 species across 24 countries. Fisher's Z was used as the standardized effect size, and a series of weighted mixed-effects models were compared to identify covariates that best explained variation in effects. Patterns in climate effects were complex, and were driven by spatial (latitude, elevation), temporal (time-period, age-class), and biological (range, habitat type, anadromy) variation within and among study populations. These trends were often consistent with predictions based on salmonid thermal tolerances. Namely, warming and decreased precipitation tended to reduce productivity when high temperatures challenged upper thermal limits, while opposite patterns were common when cold temperatures limited productivity. Overall, variable climate impacts on salmonids suggest that future declines in some locations may be counterbalanced by gains in others. In particular, we suggest that future warming should (1) increase salmonid productivity at high latitudes and elevations (especially >60° and >1,500m), (2) reduce productivity in populations experiencing hotter and dryer growing season conditions, (3) favor non-native over native salmonids, and (4) impact lentic populations less negatively than lotic ones. These patterns should help conservation and management organizations identify populations most vulnerable to climate change, which can then be prioritized for protective measures. Our framework enables broad inferences about future productivity that can inform decision-making under climate change for salmonids and other taxa, but more widespread, standardized, and hypothesis-driven research is needed to expand current knowledge.</p>
Data and code for "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"
<p>This data set provides data files and R code to accompany the article <em>Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR</em> published by F1000Research.</p> <p>The data consists of Reduced Representation BS-seq methylation profiles of epithelial populations from the mouse mammary gland, with n=2 biological replicates for each of three cell populations.</p> <p>RNA-seq expression profiles of luminal and basal mammary epithelial populations are also provided.</p> <p>The R code undertakes an differential methylation analysis of the BS-seq profiles and demonstrates a strong negative correlation between the differential methylation and differential expression results.</p>
Supporting code and data to reproduce analysis for: Genomic signatures of past megafrugivore-mediated dispersal in Malagasy palms
<p>Seed dispersal affects gene flow and hence genetic differentiation of plant populations. During the Late Quaternary, most fruit-eating and seed-dispersing megafauna went extinct, but whether these animals have left signatures in the population genetics of their food plants, particularly those with large, 'megafaunal' fruits (i.e., > 4 cm – megafruits), remains unclear.</p> <p>Here, we assessed the population history, genetic differentiation, and recent migration among populations of four animal-dispersed palm (Arecaceae) species with large (<em>Borassus madagascariensis</em>), medium-sized (<em>Hyphaene coriacea,</em> <em>Bismarckia nobilis</em>), and small (<em>Chrysalidocarpus madagascariensis</em>) fruits on Madagascar. We integrated double-digest restriction-site-associated DNA sequencing (ddRAD) of 167 individuals from 25 populations with (past) distribution ranges for extinct and extant seed-dispersing animals (e.g., giant lemurs, elephant birds), landscape and human impact data, and applied linear mixed-effects models to explore the drivers of genetic variation in Malagasy palms.</p> <p>Palm populations that shared more megafrugivore species in the past had lower genetic differentiation than populations that shared fewer megafrugivore species. This suggests that megafrugivore-mediated seed dispersal in the past may have led to frequent gene flow among populations. In comparison, extant frugivore diversity only decreased genetic differentiation in the small-fruited palm. Furthermore, genetic differentiation decreased with landscape connectivity (i.e., environmental suitability, forest cover and river density), and human impact (i.e., road density) has decreased genetic differentiation among populations.</p> <p><em>Synthesis: </em>Our results suggest that the legacy of megafrugivores regularly achieving long dispersal distances is still reflected in the population genetics of palms that were formerly dispersed by such animals. Furthermore, low genetic differentiation was possibly maintained after the megafauna extinctions through alternative dispersal (e.g., human- or river-mediated), long generation times, and long lifespans of these megafruit palms. Our study illustrates how species interactions that happened >1000 years ago can leave imprints in population genetics.</p>
DataSet & R code used for the analysis of "Mechanisms of mobbing call recognition: Exploring featural decoding in great tits"
<p>Data and R code used in a playback experiment exploring the mechanisms of mobbing call recognition in the great tit, Parus major. Accepted in Animal Behaviour (2024). </p> <p>This experiment aimed at testing the hypothesis of simple featural interpretation in the great tit (i.e., the fact that receivers can focus on specific acoustic features rather than complete note recognition). </p> <p>The experiment is organised with two parts: first, we test the response of great tits to artificial calls that possess either none or all of the characteristics present in their own calls (and shared with other Parids), and compare their level of response to natural mobbing calls. </p> <p>As the 'complete' treatment triggered the same level fo response than the natural calls, we then create artifical calls with only one of the four features used to create our artifical mobbing calls (large frequency range, low frequency, noise and harmonics). </p> <p> </p> <p>More information can be obtained by contacting Ambre SALIS (salis.ambre87[at]gmail.com)</p>
Data and code for "Salomon et al. 2024: Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis."
<div> <p>All data and R code for</p> <p><strong>Salomon S, Grubmüller E, Kropf P, Nickl E, Rühl A, Weigel S, Becker F, Antonio Vital AL, Laforsch C, Schott M, Mair MM. (2024). Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to <em>Daphnia</em> - a meta-analysis. <em>Microplastics and Nanoplastics</em>. (<a href="https://doi.org/10.1186/s43591-024-00088-4" target="_blank" rel="noopener">https://doi.org/10.1186/s43591-024-00088-4</a>)</strong></p> <p><em>Abstract</em></p> <p>Effects of micro- and nanoplastic particles (MNP) on organisms have been increasingly reported in recent years, with a large number of studies conducted on water fleas of the genus <em>Daphnia</em>. Most of the available studies used pristine particles that have not been exposed to the environment or to organic substances. In natural environments, however, organic substances like dissolved organic matter (DOM) attach to the MNP, forming an ecocorona on the particles’ surface. How the formation of an ecocorona influences MNP toxicity is still uncertain. While some studies suggest that DOM can mitigate the negative effects of MNP on organisms, other studies did not find such associations. In addition, it is unclear whether the DOM attached to the particles’ surface is attenuating the effects of MNP directly or whether co-exposure with DOM solved in the medium attenuates MNP toxicity indirectly, for instance by increasing Daphnia‘s resilience to stressors in general. To draw more solid conclusions about the direction and size of the mediating effect of DOM on MNP-associated immobilization in <em>Daphnia</em> spp., we synthesized evidence from the published literature and compiled 305 data points from 13 independent studies. The results of our meta-analysis show that the toxic effects of MNP are likely reduced in the presence of certain types of DOM in the exposure media. We found similar mediating effects when MNP were incubated in media containing DOM before the exposure experiments, although to a lesser extent. Future studies designed to disentangle the effects of DOM attached to the MNP from the general effects of DOM in the exposure medium will contribute to a deeper mechanistic understanding of MNP toxicity in nature and enhance the reliability of MNP risk assessment.</p> </div>
Analysis code and data for the morphometrics and kinematics of tube feet
<p>Hydrostatic skeletons, such as an elephant trunk or a squid tentacle, permit the transmission of mechanical work through a soft body. Despite the ubiquity of these structures among animals, we generally do not understand how differences in their morphology affect their mechanical properties. Therefore, the present study used mathematical modeling, morphometrics, and kinematics to understand the transmission of force and displacement in the tube feet of the juvenile six-rayed star <em>Leptasterias</em> <em>sp.</em> An inverse-dynamic analysis revealed that the forces generated by the feet during crawling primarily serve to overcome the submerged weight of the body. This load was disproportionately generated by the feet at more proximal positions along each ray, which were used more frequently for crawling. Due to a combination of mechanical advantage and muscle mass, these proximal feet exhibited a greater capacity for force generation than the distal feet. However, the higher displacement advantage of the more elongated distal feet offer a superior ability to extend the feet into the environment. Therefore, the morphology of tube feet demonstrates a gradient in gearing along each ray that matches their role in behavior.</p>
Data and code for behavioral analysis of: Structural and Molecular Properties of Insect Type II Motor Axon Terminals.
<p>Data and code for behavioral analysis of: Structural and Molecular Properties of Insect Type II Motor Axon Terminals.</p> <p>v1.2: typos corrected and all files available in a single .zip file for download</p>
Improving source code change set analysis by using a visual tool. Controlled experiment dataset.
<p>Modern software development is performed by developing features in isolated branches by each member of a software development team. When these branches need to be integrated, they have to be manually reviewed by an integrator. Source code reviewing can be a tedious and time consuming task, which is normally performed by hand reviewing a textual diff of the change set.</p> <p>The difficulty of reviewing source code changes can have a negative impact on the accep- tance of these changes. It has been shown that this can imply the rejection of important bug fixes for a software project.</p> <p>In order to facilitate the task of reviewing source code change sets, we designed and implemented a visual tool. Our visual tool helps in assessing source code change sets by providing different views of the change set: an overall overview of the change set with metrics, and a visualization representing the structural changes in the source code. We evaluated our visual tool by performing a controlled experiment with software practitioners.</p> <p>Our experimental results show no significant differences between using our visual tool and a textual diff tool in the following terms: time of analysis, precision of the analysis, and inference of intention of changes. However, we did find a positive user perception, and a reduced mental load when using our visual tool.</p> <p>Anonymized datasets with the answers to the controlled experiments for evaluating the Git Thermite visual tool for assessing source code change sets. Copies of these datasets are provided in both, CSV format, and OpenDocument format.</p> <p>Exact copies of the learning materials that was provided to the participants during the execution of the controlled experiments is also included along the dataset.</p>
Fig. 3 in Phylogenetic analysis of the Common Krait (Bungarus caeruleus) in Pakistan based on mitochondrial and nuclear protein coding genes
Fig. 3. Mitochondrial and nuclear genes (ND4, Cyt b, COI, 12S rRNA, 16S rRNA, C-mos, RAG-1, and NT3) Bayesian phylogeny for Common Krait (Bungarus caeruleus).
Fig. 2 in Phylogenetic analysis of the Common Krait (Bungarus caeruleus) in Pakistan based on mitochondrial and nuclear protein coding genes
Fig. 2. Mitochondrial and nuclear genes (ND4, Cyt. b, COI, 12S rRNA, 16S rRNA, C-mos, RAG-1, NT3, and BDNF) based Maximum Likelihood phylogeny for Common Krait (Bungarus caeruleus).
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.