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328 results for “Analysis results”
Supplemental Results for Assembly, Annotation, and Analysis from HiFi reads of Gulf Toadfish Genome and Transcriptome fOpsBet2.1
<p>This repository contains gzipped tarballs of the results of the various assembly, annotation, and analysis steps performed during the assembly of the fOpsBet2.1 genome assembly for Opsanus beta at the University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science for the McDonald Toadfish Lab. These results are too numerous to include as supplemental data for a journal publication and so are available here for review. In this repository you will find results for:</p><p>Scripts:</p><p>-all bash and LSF scheduler job scripts used as part of the analysis, both exploratory and final. </p><p>QC:</p><p>-GenomeScope2 estimation of genome metrics from HiFi Reads</p><p>-QUAST genome statistics for each assembly step</p><p>-BUSCO completeness assessments for each assembly step </p><p>-inspector logs for polishing of initial assembly</p><p>-logs from Kraken2 contaminant screen</p><p>Assembly and Scaffolding:</p><p>-ntLINKS logs and intermediates for initial scaffolding</p><p>-ragtag logs and metrics for super-scaffolding to the ThaAma1.1 T. amazonica reference assembly</p><p>-mitoHIFI results for mitogenome assembly from HiFi reads, primary assembly, and purged alternate assembly</p><p>Annotation:</p><p>-PASA directory with full input and output for SQLite PASA assembly of transcriptome for gene predictors</p><p>-Results folder for Funannotate::annotate for gene models, annotations, and CDS/mRNA/protein fastas</p><p>-InterProSCan5 results for protein annotation used as input into Funannotate</p><p>-ghostKOALA KEGG assignment results for predicted proteins from funannotate results</p><p>Repetitive Elements:</p><p>-tidk telomere repeat analysis results</p><p>-TRAH satellite DNA analysis with subsequent analysis with HiCAT and StainedGlass</p><p>-RepeatModeler results for de novo TE prediction</p><p>-repclassifier results for TE curation</p><p>Comparative Analysis:</p><p>-OrthoFinder ortholog search for O. beta to several other vertebrates</p><p>-CAFE5 gene family expansion and contraction of Orthogroups from OrthoFinder results</p><p> </p>
Results of a Galaxy metagenomic analysis of bee gut microbiome data from PRJNA977416
<p>This dataset contains the outputs of a metagenomic Galaxy workflow run on the raw data of the project PRJNA977416, including the CSV file of associated metadata and the workflow.ga used for the analysis.</p> <p>Firstly, it has information on taxonomic assignment with :</p> <ul> <li>the reports of all samples for Kraken2, Bracken, and MetaPhlan taxonomic profilers. </li> <li>two tabular files obtained with Taxpasta, which merge samples and standardize taxonomic abundances.</li> <li>for the Bracken standardised abundance, a file with the measures of alpha diversity calculated </li> <li>two HTML files giving access to the Krona diagram for this taxonomic composition.</li> </ul> <p>Secondly, it contains functional informations with :</p> <ul> <li>a tabular file with the relative abundance of all GO terms for all samples</li> <li>a directory detailing pathways and genes families detected.</li> </ul>
BRAIN Journal-Sentiment Analysis on Embedded Systems Blended Courses-Figure 2. Twitter sentiment analysis results
<p> In order to validate our results, the next step was to extract the sentiment analysis from Tweeter’s tweets (Figure 2) which are based on blending embedded systems-related courses. The obtained polarity is positive, so this results shows not only that students appreciated this in a positive manner, but also that the proposed technique for integrating MOOCs into embedded systems courses is a viable one. </p>
BRAIN Journal-Sentiment Analysis on Embedded Systems Blended Courses-Figure 1. Semantria result
<p>In Figure 1 the Semantria output is presented, having a positive polarity, with a score of 0.218. What is interesting to note here are the keywords extracted from students’ feedback. They noticed the integration of MOOCs in the Embedded Systems course as positive due to the fact that the new information is perceived as easier and the gained knowledge seems to be valuable. Students are affected by too many concepts and also by the idea of paying for the course.</p>
QT-IGC Meta-Analysis Results
<p>Meta-analysis results from the QT-IGC meta-analysis of QT interval duration. The manuscript detailing the generation and analysis of these results can be found here (https://www.nature.com/articles/ng.3014, Nature Genetics) and here (<a href="https://paperpile.com/shared/JEVaXW">https://paperpile.com/shared/JEVaXW</a>).</p> <p>Column names:</p> <ol> <li>SNP - SNP identifier (note that these will be on a much older dbSNP build!)</li> <li>CHR - Chromosome</li> <li>POS - Position, hg18</li> <li>A1 - minor allele in HapMap 2</li> <li>A2 - other allele in HapMap 2</li> <li>HAPMAP_A1_FREQ - frequency of A1 in HapMap</li> <li>CODED_ALLELE - the coded allele in the meta. All stats refer to this allele.</li> <li>NONCODED_ALLELE - other allele</li> <li>CODED_ALLELE_FREQ - frequency of the coded allele</li> <li>N_EFF - effective sample size</li> <li>Z_SQRTN - Z-score of the SNP in sample size meta-analysis</li> <li>P_SQRTN - P-value of the SNP in sample size meta-analysis</li> <li>BETA_FIXED - Beta of coded allele in fixed effects meta-analysis</li> <li>SE_FIXED - standard error of coded allele in fixed effects meta-analysis</li> <li>Z_FIXED - z-score of coded allele in fixed effects meta-analysis</li> <li>P_FIXED - p-value in fixed effects meta-analysis</li> <li>BETA_LOWER_FIXED - lower estimate of the beta, fixed effects</li> <li>BETA_UPPER_FIXED - upper estimate of the beta, fixed effects</li> <li>BETA_RANDOM - beta of coded allele in random effects meta-analysis</li> <li>SE_RANDOM - standard error of the coded allele in random effects meta-analysis</li> <li>Z_RANDOM - z-score from random effects meta-analysis</li> <li>P_RANDOM - p-value from random effects meta-analysis</li> <li>BETA_LOWER_RANDOM - lower estimate of the beta, random effects meta</li> <li>BETA_UPPER_RANDOM - upper estimate of the beta, random effects meta</li> <li>COCHRANS_Q - Cochran's test of heterogeneity, Q statistic</li> <li>DF - degrees of freedom for Cochran's Q test</li> <li>P_COCHRANS_Q - p-value of Cochran's Q test</li> <li>I_SQUARED - I-squared stat, test of heterogeneity</li> <li>TAU_SQUARED - Tau-squared, test of heterogeneity</li> <li>DIRECTIONS - directions of the beta in each of the cohorts used in meta-analysis. Cohorts are in the same order as in the params file provided in the related GitHub repo (https://github.com/saralpulit/QTIGCmeta)</li> <li>GENES_1000KB - Genes within 1000kb of the SNP, according to RefSeq</li> <li>NEAREST_GENE - Gene closest to the SNP, according to RefSeq</li> <li>FUNCTION - function of the SNP, if relevant</li> <li>CAVEAT - any relevant caveats, e.g., A/T or C/G SNPs with >40% minor allele frequency</li> </ol>
Results of TIMES model & inputs and outputs of the multicriteria and portfolio analysis
<p>These datasets contain the underlying data for the following publication: <strong>Energy efficiency promotion in Greece in light of risk: Evaluating policies as portfolio assets, Energy, https://doi.org/10.1016/j.energy.2018.12.180</strong></p>
Text-fig. 1. "Plant screen" scheme of complete results of the IPR-vegetation analysis derived from the database. in The Integrated Plant Record Vegetation Analysis: Internet Platform And Online Application
Text-fig. 1. "Plant screen" scheme of complete results of the IPR-vegetation analysis derived from the database.
Fig. 4 – Cluster analysis results for the distance from which ants mobilize from the nest. 4 in Mobilization Strategies in Ants (Hymenoptera: Formicidae)
Fig. 4 – Cluster analysis results for the distance from which ants mobilize from the nest. 4th cluster: F cin – Formica cinerea; 3rd cluster: F. fus – F. fusca; M. rub – Myrmica rubra; M. mut – Messor muticus; M. rug – Myrmica ruginodis; L. bru – Lasius brunneus; D. qua – Dolichoderus quadripunctatus; L. nig – Lasius niger; L. pla – L. platythorax; L. neg U – L. neglectus; T. cae – Tetramorium caespitum; T. err – Tapinoma erraticum; Temn – Temnothorax sp.; P. pal – Plagiolepis pallescens; L. ace – Leptothorax acervorum; S. fug – Solenopsis fugax; P. tau – Plagiolepis tauricus; T. arm – Tetramorium armatum; M. sal – Myrmica salina; M. spe – M. specioides; F. cun – Formica cunicularia; L. ema – Lasius emarginatus; F. ruf – Formica rufibarbis; F. cla – F. clara; C. aet – Camponotus aethiops; 2nd cluster: F. tru – Formica truncorum; L. ful – Lasius fuliginosus; C. vag – Camponotus vagus; F. pra – Formica pratensis; 1st cluster: F. rufa – Formica rufa; F. pol – F. polyctena; C. sub U – Crematogaster subdentata.
Results files and R objects for Gilmore et al 2024 SNORD116 analysis
Open the record for dataset details and reuse information.
Quantitative results of the analysis of human bioengineered tissues corresponding to the work "Generation of tissue-like models of human bilayered tissues functionalized with olive oil components"
<p>This file contains the raw dataset generated in the work entitled "GENERATION OF NOVEL TISSUE-LIKE MODELS OF HUMAN BILAYERED TISSUES FUNCTIONALIZED WITH BIOACTIVE COMPONENTS OBTAINED FROM OLIVE OIL". These results correspond to the quantification of the histological results obtained in this work.</p>
Deliverable 1.1.1.1 BEL-Float project | Dataset containing the results of numerical simulations (motions, forces) of the operational performance analysis - Part 1: Operational scenario with 6.0 m significant wave height
<p>This dataset contains the results of OpenFAST simulations performed on the DeepCwind OC4 semi-submersible combined with the 5MW NREL turbine for various wind and wave conditions. The basis of the OpenFAST input files are taken from <a href="https://github.com/OpenFAST/r-test/tree/main/glue-codes/openfast/5MW_OC4Semi_WSt_WavesWN">OpenFAST r-test GitHub repository (5MW_OC4Semi_WSt_WavesWN)</a> and adapted to simulate various wind and wave conditions. The turbulent wind field as the input to the InflowWind module is generated using <a href="https://www.nrel.gov/wind/nwtc/turbsim.html">TurbSim</a>. The simulations are performed on a modified version of OpenFAST v3.5.3 to which adaptation to the code is made to extract additional Morison drag output up to 16 cylindrical members. This adapted code is <a href="https://github.com/abkpribadi/openfast/tree/Morison_additional_output">uploaded on GitHub as a branch from a forked OpenFAST repository</a>. In total there are 1152 simulation results consists of 768 irregular waves and 384 regular waves cases. The complete dataset is divided into 9 sub-datasets to which this is part number 1. A report describing this dataset is available on the BEL-Float project website: https://www.owi-lab.be/bel-float.</p> <p> </p> <p> </p> <p> </p>
Deliverable 1.1.1.1 BEL-Float project | Dataset containing the results of numerical simulations (motions, forces) of the operational performance analysis - Part 2: Operational scenario with 4.5 m significant wave height
<p>This dataset contains the results of OpenFAST simulations performed on the DeepCwind OC4 semi-submersible combined with the 5MW NREL turbine for various wind and wave conditions. The basis of the OpenFAST input files are taken from <a href="https://github.com/OpenFAST/r-test/tree/main/glue-codes/openfast/5MW_OC4Semi_WSt_WavesWN">OpenFAST r-test GitHub repository (5MW_OC4Semi_WSt_WavesWN)</a> and adapted to simulate various wind and wave conditions. The turbulent wind field as the input to the InflowWind module is generated using <a href="https://www.nrel.gov/wind/nwtc/turbsim.html">TurbSim</a>. The simulations are performed on a modified version of OpenFAST v3.5.3 to which adaptation to the code is made to extract additional Morison drag output up to 16 cylindrical members. This adapted code is <a href="https://github.com/abkpribadi/openfast/tree/Morison_additional_output">uploaded on GitHub as a branch from a forked OpenFAST repository</a>. In total there are 1152 simulation results consists of 768 irregular waves and 384 regular waves cases. The complete dataset is divided into 9 sub-datasets to which this is part number 2. A report describing this dataset is available on the BEL-Float project website: https://www.owi-lab.be/bel-float.</p>
Deliverable 1.1.1.1 BEL-Float project | Dataset containing the results of numerical simulations (motions, forces) of the operational performance analysis - Part 8: Damaged scenario with 1.5 m significant wave height
<p>This dataset contains the results of OpenFAST simulations performed on the DeepCwind OC4 semi-submersible combined with the 5MW NREL turbine for various wind and wave conditions. The basis of the OpenFAST input files are taken from <a href="https://github.com/OpenFAST/r-test/tree/main/glue-codes/openfast/5MW_OC4Semi_WSt_WavesWN">OpenFAST r-test GitHub repository (5MW_OC4Semi_WSt_WavesWN)</a> and adapted to simulate various wind and wave conditions. The turbulent wind field as the input to the InflowWind module is generated using <a href="https://www.nrel.gov/wind/nwtc/turbsim.html">TurbSim</a>. The simulations are performed on a modified version of OpenFAST v3.5.3 to which adaptation to the code is made to extract additional Morison drag output up to 16 cylindrical members. This adapted code is <a href="https://github.com/abkpribadi/openfast/tree/Morison_additional_output">uploaded on GitHub as a branch from a forked OpenFAST repository</a>. In total there are 1152 simulation results consists of 768 irregular waves and 384 regular waves cases. The complete dataset is divided into 9 sub-datasets to which this is part number 8. A report describing this dataset is available on the BEL-Float project website: https://www.owi-lab.be/bel-float.</p>
Deliverable 1.1.1.1 BEL-Float project | Dataset containing the results of numerical simulations (motions, forces) of the operational performance analysis - Part 7: Damaged scenario with 3.0 m significant wave height
<p>This dataset contains the results of OpenFAST simulations performed on the DeepCwind OC4 semi-submersible combined with the 5MW NREL turbine for various wind and wave conditions. The basis of the OpenFAST input files are taken from <a href="https://github.com/OpenFAST/r-test/tree/main/glue-codes/openfast/5MW_OC4Semi_WSt_WavesWN">OpenFAST r-test GitHub repository (5MW_OC4Semi_WSt_WavesWN)</a> and adapted to simulate various wind and wave conditions. The turbulent wind field as the input to the InflowWind module is generated using <a href="https://www.nrel.gov/wind/nwtc/turbsim.html">TurbSim</a>. The simulations are performed on a modified version of OpenFAST v3.5.3 to which adaptation to the code is made to extract additional Morison drag output up to 16 cylindrical members. This adapted code is <a href="https://github.com/abkpribadi/openfast/tree/Morison_additional_output">uploaded on GitHub as a branch from a forked OpenFAST repository</a>. In total there are 1152 simulation results consists of 768 irregular waves and 384 regular waves cases. The complete dataset is divided into 9 sub-datasets to which this is part number 7. A report describing this dataset is available on the BEL-Float project website: https://www.owi-lab.be/bel-float.</p>
Deliverable 1.1.1.1 BEL-Float project | Dataset containing the results of numerical simulations (motions, forces) of the operational performance analysis - Part 5: Damaged scenario with 6.0 m significant wave height
<p>This dataset contains the results of OpenFAST simulations performed on the DeepCwind OC4 semi-submersible combined with the 5MW NREL turbine for various wind and wave conditions. The basis of the OpenFAST input files are taken from <a href="https://github.com/OpenFAST/r-test/tree/main/glue-codes/openfast/5MW_OC4Semi_WSt_WavesWN">OpenFAST r-test GitHub repository (5MW_OC4Semi_WSt_WavesWN)</a> and adapted to simulate various wind and wave conditions. The turbulent wind field as the input to the InflowWind module is generated using <a href="https://www.nrel.gov/wind/nwtc/turbsim.html">TurbSim</a>. The simulations are performed on a modified version of OpenFAST v3.5.3 to which adaptation to the code is made to extract additional Morison drag output up to 16 cylindrical members. This adapted code is <a href="https://github.com/abkpribadi/openfast/tree/Morison_additional_output">uploaded on GitHub as a branch from a forked OpenFAST repository</a>. In total there are 1152 simulation results consists of 768 irregular waves and 384 regular waves cases. The complete dataset is divided into 9 sub-datasets to which this is part number 5. A report describing this dataset is available on the BEL-Float project website: https://www.owi-lab.be/bel-float.</p>
Deliverable 1.1.1.1 BEL-Float project | Dataset containing the results of numerical simulations (motions, forces) of the operational performance analysis - Part 6: Damaged scenario with 4.5 m significant wave height
<p>This dataset contains the results of OpenFAST simulations performed on the DeepCwind OC4 semi-submersible combined with the 5MW NREL turbine for various wind and wave conditions. The basis of the OpenFAST input files are taken from <a href="https://github.com/OpenFAST/r-test/tree/main/glue-codes/openfast/5MW_OC4Semi_WSt_WavesWN">OpenFAST r-test GitHub repository (5MW_OC4Semi_WSt_WavesWN)</a> and adapted to simulate various wind and wave conditions. The turbulent wind field as the input to the InflowWind module is generated using <a href="https://www.nrel.gov/wind/nwtc/turbsim.html">TurbSim</a>. The simulations are performed on a modified version of OpenFAST v3.5.3 to which adaptation to the code is made to extract additional Morison drag output up to 16 cylindrical members. This adapted code is <a href="https://github.com/abkpribadi/openfast/tree/Morison_additional_output">uploaded on GitHub as a branch from a forked OpenFAST repository</a>. In total there are 1152 simulation results consists of 768 irregular waves and 384 regular waves cases. The complete dataset is divided into 9 sub-datasets to which this is part number 6. A report describing this dataset is available on the BEL-Float project website: https://www.owi-lab.be/bel-float.</p>
Deliverable 1.1.1.1 BEL-Float project | Dataset containing the results of numerical simulations (motions, forces) of the operational performance analysis - Part 4: Operational scenario with 1.5 m significant wave height
<p>This dataset contains the results of OpenFAST simulations performed on the DeepCwind OC4 semi-submersible combined with the 5MW NREL turbine for various wind and wave conditions. The basis of the OpenFAST input files are taken from <a href="https://github.com/OpenFAST/r-test/tree/main/glue-codes/openfast/5MW_OC4Semi_WSt_WavesWN">OpenFAST r-test GitHub repository (5MW_OC4Semi_WSt_WavesWN)</a> and adapted to simulate various wind and wave conditions. The turbulent wind field as the input to the InflowWind module is generated using <a href="https://www.nrel.gov/wind/nwtc/turbsim.html">TurbSim</a>. The simulations are performed on a modified version of OpenFAST v3.5.3 to which adaptation to the code is made to extract additional Morison drag output up to 16 cylindrical members. This adapted code is <a href="https://github.com/abkpribadi/openfast/tree/Morison_additional_output">uploaded on GitHub as a branch from a forked OpenFAST repository</a>. In total there are 1152 simulation results consists of 768 irregular waves and 384 regular waves cases. The complete dataset is divided into 9 sub-datasets to which this is part number 4. A report describing this dataset is available on the BEL-Float project website: https://www.owi-lab.be/bel-float.</p>
Deliverable 1.1.1.1 BEL-Float project | Dataset containing the results of numerical simulations (motions, forces) of the operational performance analysis - Part 3: Operational scenario with 3.0 m significant wave height
<p>This dataset contains the results of OpenFAST simulations performed on the DeepCwind OC4 semi-submersible combined with the 5MW NREL turbine for various wind and wave conditions. The basis of the OpenFAST input files are taken from <a href="https://github.com/OpenFAST/r-test/tree/main/glue-codes/openfast/5MW_OC4Semi_WSt_WavesWN">OpenFAST r-test GitHub repository (5MW_OC4Semi_WSt_WavesWN)</a> and adapted to simulate various wind and wave conditions. The turbulent wind field as the input to the InflowWind module is generated using <a href="https://www.nrel.gov/wind/nwtc/turbsim.html">TurbSim</a>. The simulations are performed on a modified version of OpenFAST v3.5.3 to which adaptation to the code is made to extract additional Morison drag output up to 16 cylindrical members. This adapted code is <a href="https://github.com/abkpribadi/openfast/tree/Morison_additional_output">uploaded on GitHub as a branch from a forked OpenFAST repository</a>. In total there are 1152 simulation results consists of 768 irregular waves and 384 regular waves cases. The complete dataset is divided into 9 sub-datasets to which this is part number 3. A report describing this dataset is available on the BEL-Float project website: https://www.owi-lab.be/bel-float.</p>
Quantitative results of the analysis of two types of bone particles corresponding to the work "A comprehensive analysis of two types of xenogeneic bone particles for use in maxillofacial bone regeneration therapies"
<p>This dataset corresponds to the quantitative data generated in the work entitled "A comprehensive analysis of two types of xenogeneic bone particles for use in maxillofacial bone regeneration therapies".</p> <p>Regeneration of maxillofacial bone structures is challenging. One of the strategies applied to bone damage repair is the use of bone filler particles, and different types of these particles have been tested. In this work, we analyzed the regenerative potential of deproteinized bone particles (DP) and collagen-based bone particles (CP) to determine the potential of each biomaterial in bone repair. Results of the structural analysis using scanning electron microscopy and 3D scanning showed that DP and CP were structurally similar, and consisted of a heterogeneous mixture of bone particles of different sizes and shapes. Then, ex vivo analyses using morphological evaluation, LIVE & DEAD and quantification of DNA released to the medium demonstrated that CP and DP were highly biocompatible when used in direct and in indirect contact with human cells, at 24, 48 and 72h of follow-up. Then, when both particles were grafted for 2 months on Wistar rats in which a critical defect had been generated at the mandible bone. Results of the computed tomography analysis showed a significant reduction of the bone defect in the CP group, but not in the DP group, as compared with negative controls devoid of any bone particles. Histological analysis of the graft area revealed that both particles were biocompatible in vivo, and a regenerative tissue with collagen fibers and mineralized spots was found in CP and DP, with higher number of mineralized spots in DP. Histochemistry and immunohistochemistry analyses confirmed the presence of collagen, proteoglycans and osteocalcin at the regeneration area of CP and DP. In general, these results confirm the biocompatibility of both types of particles and that both were able to induce maxillofacial bone regeneration, especially in the case of CP. Future studies should determine their clinical usefulness in patients with cleft palate, mandibular damage and other maxillofacial applications.</p>
Complete results of Procedure section in manuscript "PathML: A unified framework for whole-slide image analysis with deep learning"
<p>The results from a complete run of the Procedure section of the paper "PathML: A unified framework for whole-slide image analysis with deep learning".</p>
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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.