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4,694 results for “data analysis”
A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases_NGS data analysis
<p>These data files are associated with the NGS analysis done in the publication :"A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases". This compressed file contains the raw file as well as the processed files to arrive at the conclusions published. The python scripts used for processing the data are available on github (link provided in the manuscript).</p>
Assemblies, associated annotation files, and analysis source data of Platanus x acerifloia genome
<p><em>Platanus</em> <span>× </span><em>acerifolia </em>(London plane; Platanaceae) is a major ornamental tree used worldwide. Platanaceae is one of the last early-diverging eudicot families without a complete nuclear genome assembly. Here, we assembled a high-quality, chromosome-level reference genome for <em>P.</em> <span>× </span><em>acerifolia.</em></p>
Model Data and Diagnostics used for the Lake Victoria Process Analysis
<p>Model data and derived diagnostics used in the Lake Victoria analysis, from Unified Model output. © Crown Copyright, Met Office</p>
The derived data in manuscript Oblique impact adjacent to Chang'E-5 landing site: Fine-scale analysis and implication on the provenance of returned samples
<p>This website contains the derived data in the <em>manuscript <span>Oblique impact adjacent to Chang’E-5 landing site: </span><span>F</span><span>ine-scale analysis and implication on the provenance of returned samples </span></em>by <span>Wenhui Wu</span><span>, </span><span>Zhaopeng Chen</span><span>, Xin Ren</span><span>, Dawei Liu</span><span>,</span><span> </span><span>Xingguo Zeng, Yuan Chen, Wangli Chen, Wei Yan, Bin Liu,Xiaoxia Zhang, Jianjun Liu</span> for <em><span>Journal of Geophysical Research: Planets</span></em></p>
Peptidoform analysis of IP-MS data allows detection of differentially present bait proteoforms
<p>Datasets supporting iPTMs manuscript (https://doi.org/10.1101/2024.01.23.576810)</p>
Data used for analysis in "Calibrating tropical forest coexistence in ecosystem demography models using multi-objective optimization through population-based parallel surrogate search"
Open the record for dataset details and reuse information.
Distance Tuneable Integral Membrane Protein Containing Floating Bilayers via In Situ Directed Self-Assembly : Data and Analysis Scripts
<p>Neutron Reflectometry data and analysis scripts (for RasCal software) and Quartz Crystal Microbalance data and plotting script for data shown in Figures 1, 3, 4 and 5 of the Article: Distance Tuneable Integral Membrane Protein Containing Floating Bilayers via In Situ Directed Self-Assembly.</p>
Raw data and correlation analysis of physiological data sampled from Atlantic halibut (Hippoglossus hippoglossus) for the development of a PBPK model
<p>Raw data sampled from Atlantic halibut <em>(Hippoglossus hippoglossus)</em> for the characterization of physiological parameters for the development of a species-specific physiology-based pharmacokinetic (PBPK) model. Additionally, the document containes imputed data for a PCA analysis and correlation coefficients and the related p-values from a correlation analysis. </p>
Data used in the quantitative analysis and absolute and relative frequency
<p>Data used in the quantitative analysis and absolute and relative frequency</p>
Figures - Semantic analysis of web archive historical data 1983 "Marche pour l'égalité et contre le racisme"
Open the record for dataset details and reuse information.
Sociotechnical Dynamics in Open Source Smart Contract Repositories: An Exploratory Data Analysis of Curated High Market Value Projects
<p>This is the replication package for the paper “Sociotechnical Dynamics in Open Source Smart Contract Repositories: An Exploratory Data Analysis of Curated High Market Value Projects”.</p> <p>In project_curation_selection, there is the curation process of the 100 selected projects including the identification of GitHub repositories and classification of evolution scenarios. </p> <p>In distribution_commits_issues_contributors_market_value_before_after_deploy, data collection from GitHub projects includes the distribution of total commits, contributors, and issues before and after deployment of each investigated project. </p> <p>In analysis_commit_messages, there is qualitative analysis of commit message content from all investigated projects. </p> <p>In the analysis_contributors section, the data focuses on analyzing the profiles of each GitHub contributor involved in the investigated projects.</p> <p>In analysis_market_value_by_project, data refers to the market value and volume of each investigated project. </p> <p>In codes, there are scripts used to obtain the analyzed data.</p> <p> </p>
Figure 2. Implied weighting analysis, one tree obtained with concavity constant value k in New and revised taxa of Neotropical Diplotaxini (Coleoptera: Melolonthidae): do they change the existing relationships? Revisiting systematics with morphological and molecular data
Figure 2. Implied weighting analysis, one tree obtained with concavity constant value k = 8.750. The numbers displayed in each node correspond to the value of relative Bremer and symmetric resampling supports (above and below, respectively).
SMART Analysis Data
<p>This is the processed data associated with simulations from the <a href="https://github.com/RangamaniLabUCSD/smart-comp-sci.git">SMART comp sci repository</a>. There are five separate folders, one for each of the examples showcased therein: `mechanotransduction`, `dendritic-spine`, `cru`, `mito`, and `phosphorylation`.</p> <p>These folders contain numpy files with average concentrations for each variable, as well as json files containing information stored from different simulation runs and output plots. All plots can be reproduced using files from the SMART Comp Sci repository after downloading the data here and placing it in a folder `analysis_data` within the local repository.</p>
Data from: D3.2. Multi-criteria decision analysis (MCDA) for selection and location of hybrid solutions
Open the record for dataset details and reuse information.
FLIM Data and analysis of the hands-on sessions "CF44-1 Label-free metabolic FLIM with 2 photon excitation"
<p>This FLIM dataset on HeLa cells and human astrocytes was acquired during the hands-on sessions <em>CF44-1 Label-free metabolic FLIM with 2 photon excitation</em> during the <a href="https://www.bioimaging.bmc.med.uni-muenchen.de/gerbiflim2024/flimprogram/index.html">German BioImaging </a><a href="https://www.bioimaging.bmc.med.uni-muenchen.de/gerbiflim2024/flimprogram/index.html">workshop on FLIM in Munich</a>.</p> <p>The FLIM data are analyzed with the open source software FLUTE available on GitHub: <a href="https://github.com/LaboratoryOpticsBiosciences/FLUTE"><strong><em>https://github.com/LaboratoryOpticsBiosciences/FLUTE</em></strong></a></p> <p>and published on Biological imaging Journal: <a href="https://www.cambridge.org/core/journals/biological-imaging/article/flute-a-python-gui-for-interactive-phasor-analysis-of-flim-data/862F290EC14187741BDA6B58E9868FA2"><strong><em>Gottlieb, D., Asadipour, B., Kostina, P., Ung, T., & Stringari, C. (2023). FLUTE: A Python GUI for interactive phasor analysis of FLIM data. Biological Imaging, 1-22. doi:10.1017/S2633903X23000211</em></strong></a></p>
Modelling input data for the case study of the paper "Uncertainty-Based Market-Clearing Models: A Comparative Analysis of the Dutch, French, and German Markets".
<p>This data package includes the modelling input data to replicate the results of the case study included in the paper "Uncertainty-Based Market-Clearing Models: A Comparative<br>Analysis of the Dutch, French, and German Markets". </p> <p>The case study models the Dutch, French and German day-ahead electricity markets, in which the existing capacities of electricity generation and upward- and downward reserve capacities are considered, in addition to 105 wind output realization scenarios for each simulation day. A detailed description of the case study is provided in the readme file.</p> <p>This supplementary data package includes the following files:</p> <p>- Meta Data – Netherlands.xlsx: Dataset containing the meta data for the Dutch case study</p> <p>- Meta Data – France.xlsx: Dataset containing the meta data for the French case study</p> <p>- Meta Data – Germany.xlsx: Dataset containing the meta data for the German case study</p> <p>- Readme.txt: Includes a detailed description of the data packages</p>
Gene expression data from qPCR analysis of molting relevant genes in Calanus finmarchicus utilizing double delta-Ct method
<p>Gene expression data from qPCR analysis of molting relevant genes in Calanus finmarchicus utilizing double delta-Ct method for calculations of fold change and mean fold change. </p>
Transcriptome data of the analysis of two isolates of the tomato pathogen Cladosporium fulvum during host interaction
<p>This dataset contains sequences of assembled transcripts from isolates Race 5 and Race 4 of the tomato pathogen Cladosporium fulvum during interaction with its host.</p> <p><strong>transcripts:</strong> Assembled transcripts in FASTA and GTF fomats. The GTF files have coordinates of the transcripts in the reference genomes of isolates Race 5 (GCA_020509005.2) and Race 4 (GCA_035196885.1). The other FASTA files include the predicted open reading frames (ORFs) in the transcripts. The nucleotide coding sequence and translated amino acid sequences of the ORFs are in separated FASTA files. In the file names isolate Race 5 is indicated with '*R5*', and isolate Race 4 is indicated with '*R4*'. Description of the files is shown below:</p> <ul> <li><code>representatives_R4_diff_introns.fasta</code>: full-length transcript sequences from isolate Race 4.</li> <li><code>representatives_R5_diff_introns.fasta</code>: full-length transcript sequences from isolate Race 5.</li> <li><code>representatives_R4_diff_introns.gtf</code>: coordinates of the transcripts from isolate Race 4 in the genome of Race 4.</li> <li><code>representatives_R5_diff_introns.gtf</code>: coordinates of the transcripts from isolate Race 5 in the genome of Race 5.</li> <li><code>representatives_orfs_aa_R4_diff_introns.fasta:</code> predicted protein sequences encoded in the transcripts from isolate Race 4.</li> <li><code>representatives_orfs_aa_R5_diff_introns.fasta</code>: predicted protein sequences encoded in the transcripts from isolate Race 5.</li> <li><code>representatives_orfs_cds_R4_diff_introns.fasta</code>: predicted coding sequences in the transcripts from isolate Race 4.</li> <li><code>representatives_orfs_cds_R5_diff_introns.fasta</code>: predicted coding sequences in the transcripts from isolate Race 5.</li> </ul> <p><strong>expression:</strong> Contains tab-separated files with the expression values (transcripts per million - TPM) of the transcripts from isolates Race 5 and Race 4 at specific time points (2, 4, 6, 8, 10, 12, and 14 dpi) during interaction with tomato. TPM values were estimated with the alignment-free method Salmon.</p>
Density field data & VTK files for dislocation embedding analysis
<p>The dataset includes dislocation density field results and VTK files from the discrete dislocation dynamics (DDD) simulation of an FCC-based structure (Al).</p> <p>Various loading directions in compression ([100], [110], [111], [234]) and their misorientations (-10°, -5°, 0°, +5°, +10°) were analyzed using two different initial dislocation densities in the DDD simulation.</p> <p>Post-processing was done with two different discretizations, yielding a dataset with the following description:</p> <p><strong>ddd_8res_0deg </strong>— 8x16x8 discretization data with 0° misorientation.<br><strong>ddd_8res_p5deg</strong> — 8x16x8 discretization data with +5° misorientation.<br><strong>ddd_8ress_m5deg </strong>— 8x16x8 discretization data with -5° misorientation.<br><strong>ddd_8res_p10deg</strong> — 8x16x8 discretization data with +10° misorientation.<br><strong>ddd_8res_m10deg </strong>— 8x16x8 discretization data with -10° misorientation.</p> <p><strong>ddd_16res_0deg </strong>— 16x32x16 discretization data with 0° misorientation.<br><strong>ddd_16res_p5deg </strong>— 16x32x16 discretization data with +5° misorientation.<br><strong>ddd_16ress_m5deg</strong> — 16x32x16 discretization data with -5° misorientation.<br><strong>ddd_16res_p10deg </strong>— 16x32x16 discretization data with +10° misorientation.<br><strong>ddd_16res_m10deg </strong>— 16x32x16 discretization data with -10° misorientation.</p> <p><strong>config1</strong> — \(2.5 \times 10^{13} \text{ m}^{-2}\)<br><strong>config2 </strong>— \(1 \times 10^{14} \text{ m}^{-2}\)</p> <p>This dataset complements a related publication as additional information. The link to the publication will be made available after it is published.</p>
Data from: Impacts of organic matter amendments on urban soil carbon and soil quality: A meta-analysis
<p>Organic matter amendment application is an important avenue of beneficial waste diversion and is used to improve soil quality in agricultural and urban settings. In urban regions, amendments are used to support local food production, maintain vegetation for landscaping and recreational use, and reclaim disturbed soils. Urban regions generate large quantities of wasted organic resources for potential application aiding in creating a circular nutrient economy. There is a growing interest in understanding the effects of amendments such as compost, biosolids, and biochar on soil properties in agricultural settings. Gaps remain, however, in assessing their effects in urban land uses. We conducted a literature review to assess the effects of compost, biochar, and biosolids on soil carbon and soil quality of urban soils managed for gardening, landscaping, recreation, and reclamation. Application of organic matter amendments led to an average increase of 3.6 units of soil organic matter% (SOM%). Compost and biochar improved SOM% the most, by 3.1 and 6.5 units of SOM%, respectively. Biosolids resulted in the smallest increase in SOM% but had greater nutrient benefits than other amendments. Parameters related to chemical and physical soil quality improved with the application of amendments. Gaps in the literature remain, such as assessing urban gardens, soil to depths greater than 30 cm, and the persistence of SOM in amended soils. This meta-analysis proposes that organic matter amendments are a powerful means to improve soil quality in urban regions, provide vital cobenefits to surrounding communities, and increase soil carbon storage.</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.