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466 results for “code analysis”
Data from: Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep
<p>This dataset contains additional files from the manuscript: "Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep".</p> <p>The files included are:</p> <p>- All novel lncRNA transcript annotation GTF file ( lncrnas.gtf )</p> <p>- High-confidence lncRNA gene annotation GTF file ( lncrnas_evidence.gtf )</p> <p>- All novel lncRNA transcript annotation GTF file remapped to the ARS-UI_Ramb_v2.0 genome ( lncrnas_remapped_v2.gtf )</p> <p>- Raw count estimates of the extended annotation ( rawcounts.csv )</p> <p>- TPM values of the extended annotation ( tpmcounts.csv )</p> <p>- Supplementary data to the published article (.xlsx, .pdf)</p> <p> </p>
BOREALIS Power Analysis Code and Data
<p>This contains the code and data necessary to rerun the power analysis used in testing BOREALIS.</p> <p>Borealis is an R library performing outlier analysis for count-based bisulfite sequencing data. It detects outlier methylated CpG sites from bisulfite sequencing (BS-seq). The core of Borealis is modeling Beta-Binomial distributions. This can be useful for rare disease diagnoses.</p>
Codes to replicate statistical analysis in UPLIFT project Deliverable 2.4 Synthesis report, Chapter 6
<p>Policies attempting to mitigate the effects of urban inequality, often disregard affected citizens’ experiences, and thus fail to achieve maximum impact. By incorporating these perspectives into the policy design process, the project "Urban PoLicy Innovation to address inequality with and for Future generaTions" (UPLIFT), funded under the EU Horizon 2020 program aims to find innovative interventions in a bottom-up approach. The aims of UPLIFT project are to understand patterns and trends of inequality across Europe and to understand how individuals experience and adapt to inequality through participatory research. Moreover the project will together with the communities in four locations, co-design a policy tool aimed at addressing and reducing inequality and socio-economic divisions. The activity and results of the project can be followed at <a href="https://www.uplift-youth.eu/">https://www.uplift-youth.eu/</a>.</p> <p>Deliverable 2.4 (Synthesis report: socioeconomic inequalities in different urban contexts) is the final deliverable of work package 2 of the UPLIFT project, which aims to synthetize the main outcomes of the urban reports that described the policy environment around vulnerable individuals in the fields of education, employment and housing in 16 functional urban areas of the EU. In addition section 6.2 "Statistical analysis of linkages between economic development of cities, their public policy performance and inequality outcomes" of the report provides a statistical analysis of how local economic competitiveness and the local policy context affect urban deprivation and inequality among the young in European cities. The analysis is based on data from 2006, 2009, 2012, 2015 and 2019 of the Quality of Life in European Cities survey.</p>
CARDAMOM Phenology Study: Dataset and Analysis Code
<p>This repository stores the input data, output data and analysis code for the following publication:</p> <p>Norton, A. J., Bloom, A. A., Parazoo, N. C., Levine, P. A., Ma, S., Braghiere, R. K., and Smallman, L. T.: Improved process representation of leaf phenology significantly shifts climate sensitivity of ecosystem carbon balance, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2022-1265, 2022.</p>
Datasets, reproducible codes, and results for evaluating differential expression analysis methods on population-level RNA-seq data
<p>This upload contains the necessary R codes and data to reproduce the FDR and Power results described in our correspondence "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" to Li Y, Ge X, Peng F, Li W, Li JJ, Exaggerated false positives by popular differential expression methods when analyzing human population samples, <em>Genome Biology</em> 23, 79, 2022, DOI: 10.1186/s13059-022-02648-4.</p>
Mapping literature reviews on coral health: A review map, critical appraisal, and bibliometric analysis - Data and Code
<p>Data, code, and supplementary materials for "Mapping literature reviews on coral health: A review map, critical appraisal, and bibliometric analysis" by Burke et al., published in Ecological Solutions and Evidence.</p>
Diminishing returns on labor in the global marine food system: Dataset S1 and code for analysis
<p>Dataset on the number of marine fishers 1950-2015 accompanying the manuscript "Diminishing returns on labor in the global marine food system" by K. J. N. Scherrer, Y. Rousseau, L. C. L. Teh, U. R. Sumaila and E. D. Galbraith. Includes 1) script for data analysis, 2) processed fisheries labor data set, 3) separate data file with average socioeconomic indicators by country needed for analysis, 4) data documentation. </p>
Data and analysis code from: Micro-scale geography of synchrony in a serpentine plant community
This package includes data and code to reproduce analyses of micro-scale geography of synchrony in the plant community at Jasper Ridge Biological Preserve. Plant cover and soil depth data come from long-term experimental plots established by Richard Hobbs. Plant cover is aggregated into 36 1m2 plots across three treatments (control, gopher exclosure, rabbit exclosure) from 1983 to 2015; included herein are data on the 6 most abundant species (Plantago erecta, Bromus hordeaceous, Lasthenia californica, Microseris douglasii, Vulpia microstachys, and Calycadenia multiglandulosa), total plant cover across all species, and records of gopher disturbance in the plots. The data package also includes time series of monthly precipitation and growing season Palmer’s Drought Severity Index for the same time period. An R Markdown file is included that reproduces all analyses described in the manuscript and reproduces all data figures. Data to support: Walter, Hallett et al. in review “Micro-scale geography of synchrony in a serpentine plant community
R code and data to reproduce figures from the "Multivariate autoregressive modelling and conditional simulation for temporal uncertainty analysis of an urban water system in Luxembourg" paper
<p>This repository contains the R code and data to reproduce figures from the "Multivariate autoregressive modelling and conditional simulation for temporal uncertainty analysis of an urban water system in Luxembourg" paper.</p>
Trophic-meta-analysis: Second release of tritrophic meta-analysis data, code and appendices
<p>Data, R script and appendices for "Interaction strength and the impact of introduced omnivores: A meta-analysis of introduced aquatic invasive species" submitted to Oikos</p>
A meta-analysis on global change drivers and the risk of infectious disease database and code
<p>Data and code associated with the manuscript "A Meta-analysis on Global change drivers and the risk of infectious disease".</p>
Data and code for: Nonlinear life table response analysis: Decomposing nonlinear and nonadditive population growth responses to changes in environmental drivers
<p>Life table response experiments (LTREs) decompose differences in population growth rate between environments into separate contributions from each underlying demographic rate. However, most LTRE analyses make the unrealistic assumption that the relationships between demographic rates and environmental drivers are linear and independent, which may result in diminished accuracy when these assumptions are violated. In this study, we compare the relative efficacy of linear and second-order LTRE analyses in capturing changes in population growth rate caused by environmental driver changes. To explore this question, we analyze demographic data collected for three long-lived plant species: <em>Ardisia escallonioides</em> (Pascarella & Horvitz, 1998), <em>Silene acaulis</em>, and <em>Bistorta vivipara</em> (Doak & Morris, 2010). This repository includes data files containing vital rate (survival, growth, reproduction) observations or models for our three case studies, as well as an R script in which we use these demographic data to calculate linear and second-order LTRE approximations of changes in population growth rate for each system and generate the figures we present in our paper.</p>
Post‐processed data and analysis codes for the research "Significant reduction of potential exposure to extreme marine heatwaves by achieving carbon neutrality"
<p>[Earth's Future] Oh et al. "Significant reduction of potential exposure to extreme marine heatwaves by achieving carbon neutrality"</p> <p>1. Information for Raw datasets<br>- The data of eight global climate models from the Coupled Model Intercomparison Project Phase 6 (CMIP6) can be accessed at https://esgf-node.llnl.gov/search/cmip6/, <br> and can also be accessed in Eyring et al. (2016). <br>- The NOAA OISST high resolution dataset can be obtained in Reynolds et al. (2007) or via https://psl.noaa.gov/data/gridded/data.noaa.oisst.v2.highres.html. <br>- The five ocean mask dataset can be obtained from https://reccap2-ocean.github.io/regions/. </p> <p>2. Information for Software<br>- The raw data in this study were analyzed using Fortran 90, R version 4.0.3, and Grads version 2.2.1.<br>- The Fortran 90 can be accessed at https://www.intel.com/content/www/us/en/developer/articles/tool/oneapi-standalone-components.html#fortran. <br>- The R version 4.0.3 is available from https://cran.r-project.org/bin/windows/base/old/4.0.3/. <br>- The Grads version 2.2.1 can be downloaded from http://cola.gmu.edu/grads/downloads.php.</p> <p>3. Information for Post-Processed data and Codes used in this work.<br>Please find each folder and the relevant post-processed dataset and codes.</p>
Codes and Data for "Vertically resolved analysis of the Madden-Julian Oscillation highlights the role of convective transport of moist static energy"
<p>This file contains the analysis code and a condensed version of data to reproduce figures in the paper "Vertically resolved analysis of the Madden-Julian Oscillation highlights the role of convective transport of moist static energy". </p>
DATA SET USED IN THE PHYLOGENETIC ANALYSIS ?, condition not preserved. Coding for Paraortygoides based on BMNH PAL A 6217 (holotype of P. radagasti) and SMRME 1303 (holotype of P. messelensis) in The Fossil Galliform Bird Paraortygoides from the Lower Eocene of the United Kingdom
DATA SET USED IN THE PHYLOGENETIC ANALYSIS ?, condition not preserved. Coding for Paraortygoides based on BMNH PAL A 6217 (holotype of P. radagasti) and SMRME 1303 (holotype of P. messelensis)
Supplementary datasets, data analysis code, and R tutorials for: Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs
<p>Comparative phylogenetic studies of adaptation are uncommon in biomechanics and physiology. Such studies require collecting data from many species, a challenge when data collection is experimentally intensive. Moreover, researchers struggle to employ the most biologically appropriate phylogenetic tools for identifying adaptive evolution. Here, we detail an established but greatly underutilized phylogenetic comparative framework—the Ornstein-Uhlenbeck process—that explicitly models long-term adaptation. We discuss challenges in implementing and interpreting the model, and we outline potential solutions. We demonstrate use of the model through studying the evolution of thermal physiology in treefrogs. Frogs of the family Hylidae have twice colonized the temperate zone from the tropics, and such colonization likely involved a fundamental change in physiology due to colder and more seasonal temperatures. However, which traits changed to allow colonization is unclear. We measured cold-temperature tolerance and characterized thermal performance curves in jumping for twelve species of treefrogs distributed from the Neotropics to temperate North America. We then conducted phylogenetic comparative analyses to examine how tolerances and performance curves evolved and to test whether that evolution was adaptive. We found that tolerance to low temperatures increased with the transition to the temperate zone. In contrast, jumping well at colder temperatures was unrelated to biogeography and thus did not adapt during dispersal. Overall, our paper shows how comparative phylogenetic methods can be leveraged in biomechanics and physiology to test the evolutionary drivers of variation among species.</p>
Affective, physiological, and attention restoration at a wooden desk: A pilot study (Datasets and R analysis code)
<p>This entry contains datasets and R processing and analysis code for the article <em>Affective, physiological, and attention restoration at a wooden desk: A pilot study.</em><br> <br> The analysis primarily investigates how people respond to the Mental Arithmetic Task (MAT) in terms of their affective states and physiological arousal, and how their cognitive performance changes between two task administrations. The analysis also checks whether affective, physiological, and cognitive responses differ between settings furnished with or without wood. We base our analysis on self-reported affective states, captured physiological (electrodermal and cardiovascular) activity, and results on the cognitive task (i.e., MAT).</p>
Data and analysis codes for "In vivo visualization of butterfly scale cell morphogenesis in Vanessa cardui"
<p>Butterfly scale data and data analysis codes for "In vivo visualization of butterfly scale cell morphogenesis in <em>Vanessa cardui</em>."</p> <p> </p> <p>It is recommended to download all files and folders into a single root folder for use in MATLAB.<br> This code was prepared for use in MATLAB R2019b, and some scripts or functions require the Image Processing Toolbox.</p>
Code to generate figures 3 and 4 of: "A comprehensive LFQ benchmark dataset to validate data analysis pipelines on modern day acquisition strategies in proteomics."
<p>Code to generate figures 3 and 4 of the manuscript titled "A comprehensive LFQ benchmark dataset to validate data analysis pipelines on modern day acquisition strategies in proteomics."</p> <p> </p>
WP2 Task 2.2 questionnaire analysis and coding
<p>Aggregate answers and coding for WP2 questionnaire on Design of Knowledge Reservoirs in Thematic Networks</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.