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Figure 3 from: Walton S, Livermore L, Bánki O, Cubey RWN, Drinkwater R, Englund M, Goble C, Groom Q, Kermorvant C, Rey I, Santos CM, Scott B, Williams AR, Wu Z (2020) Landscape Analysis for the Specimen Data Refinery. Research Ideas and Outcomes 6: e57602. https://doi.org/10.3897/rio.6.e57602
Figure 3 The proposed workflow technology stack for the SDR.
Figure 2 from: Walton S, Livermore L, Bánki O, Cubey RWN, Drinkwater R, Englund M, Goble C, Groom Q, Kermorvant C, Rey I, Santos CM, Scott B, Williams AR, Wu Z (2020) Landscape Analysis for the Specimen Data Refinery. Research Ideas and Outcomes 6: e57602. https://doi.org/10.3897/rio.6.e57602
Figure 2 Traffic-light results of gap analysis applied to overall proposed workflow.
Data and R script for publication: The LOKI underwater imaging system and an automatic identification model for the detection of zooplankton taxa in the Arctic Ocean
<p>This is a www.zenodo.org data and R script upload for publication:</p> <p> </p> <p>Schmid, M.S. et al., The LOKI underwater imaging system and an automatic identification model for the detection of zooplankton taxa in the Arctic Ocean. Methods in Oceanography (2016), http://dx.doi.org/10.1016/j.mio.2016.03.003</p> <p> </p> <p>Downloadable script: Script_Schmid_Mio_2016_data_upload.R</p> <p>Downloadable data: Schmid_2016_MIO_CGlac.csv</p>
Data and R-Code from: How to account for behavioral states in step-selection analysis: a model comparison
<p>This repository provides the R-code and data used for the simulation and case study of the research paper: "How to account for behavioral states in step-selection analysis: a model comparison".</p><p>The folder "<strong>Pohle_et_al_2023_BehavioralStates_iSSA_Data</strong>" contains the landscape rasters used for data generation in the simulation study, and the bank vole (<i>Myodes glareolus</i>) movement data used in the case study on bank vole interactions:</p><ul><li>landscape10.RData and landscape50.RData: Landscape rasters for the simulation study.</li><li>Vole_case_control.rds: Case-control bank vole data for the case study.</li><li>Info_replicates.rds: Information about bank vole indiviuals and corresponding replicates for the case study.</li><li>Codebook_case_study.xlsx: Codebook for the case study data sets.</li><li>Read_me.txt</li></ul><p>The folder "<strong>Pohle_et_al_2023_BehavioralStates_iSSA_RCode</strong>" contains the R-scripts for the simulation and case study:</p><ul><li>Functions.R: Functions to apply HMMs, TS-iSSAs, and HMM-iSSAs to movement data; used for the simulation and case study.</li><li>Simulation_study.R: R-Code to run the simulation study. Parallel computation is used.</li><li>Results_simulation_study.R: R-Code to create the result figures and tables for the simulation study.</li><li>Case_study.R: R-Code to run the bank vole interaction case study. Parallel computation is used.</li><li>Results_case_study.R: R-Code to create the result figures and tables for the case study.</li><li>Read_me.txt</li></ul><p>Besides the simulation and case study from the paper, the included functions (<i>Functions.R</i>) can generally be used to perform an HMM-iSSA analysis.</p><p>For the bank vole movement data without control locations, see: Schlägel, U.E. et al. (2019). Data from: Estimating interactions between individuals from concurrent animal movements [Dataset]. Dryad. <a href="https://doi.org/10.5061/dryad.rt535m8">https://doi.org/10.5061/dryad.rt535m8</a>.</p><p><strong>Acknowledgements</strong></p><p>We thank Sophie Eden, Angela Puschmann and Pauline Lange for help with the bank vole data collection and maintenance of the outdoor enclosures.</p><p> </p><p> </p>
Data and R scripts for: Variation in phenotypic plasticity across age-at-maturity genotypes in wild Atlantic salmon
<p>Data and R-scripts underlying the statistical analyses of the study. </p>
Figure 1 from: Borisenko A, Young R, Hanner R (2024) A lab-centric, workflow-based data management system for environmental DNA research. Research Ideas and Outcomes 10: e120483. https://doi.org/10.3897/rio.10.e120483
Figure 1 Schematic representation of key ontological entities of an eDNA data management system.
Gentsch et al.:Soil nitrogen and water management by winter-killed catch crops. Open data and R scripts.
<p>The file contains metadata on catch crop biomass, soil water contents, and ammonia and nitrate contents in different soil depth from the CATCHY experimental field site Asendorf. R scripts are provided for statistic evaluation of the metadata, plots for publication and spatiotemporal visualization. The article to this data set ist published in the lournal SOIL from Copernicus publisher: <a href="https://soil.copernicus.org/articles/8/269/2022/">https://soil.copernicus.org/articles/8/269/2022/</a></p>
Dryandra Carrion Flies - R script and data
<p>Carrion fly R scripts and accompanying data. </p>
Figure 2 from: Xu K-W, Han Y-T, Dong Y-R, Guo J-Q, Mao L-F, Liao W-B (2024) Asplenium guodanum (Aspleniaceae), a distinct new fern species from northern Guangdong, China, based on morphological data and molecular phylogeny. PhytoKeys 241: 191-200. https://doi.org/10.3897/phytokeys.241.122789
Figure 2 Micromorphology of Asplenium guodanum sp. nov. A–E spore F scale. Scale bar: 1 mm.
Figure 2 from: Assou D, Segniagbeto GH, Radji R, Akiti J, Pando F (2018) Monitoring data of marine turtles on the Togolese coast during 2012–2013. ZooKeys 779: 109-118. https://doi.org/10.3897/zookeys.779.26967
Figure 2 Monitoring program sites (Segniagbeto et al. 2017).
Figure 3 from: Assou D, Segniagbeto GH, Radji R, Akiti J, Pando F (2018) Monitoring data of marine turtles on the Togolese coast during 2012–2013. ZooKeys 779: 109-118. https://doi.org/10.3897/zookeys.779.26967
Figure 3 Distribution of marine turtle occurrences by species on the Togolese coast.
Figure 1 from: Assou D, Segniagbeto GH, Radji R, Akiti J, Pando F (2018) Monitoring data of marine turtles on the Togolese coast during 2012–2013. ZooKeys 779: 109-118. https://doi.org/10.3897/zookeys.779.26967
Figure 1 Region of the record Datasets of sea turtles (coastal areas of Ghana, Togo and Benin).
Figure 4 from: Assou D, Segniagbeto GH, Radji R, Akiti J, Pando F (2018) Monitoring data of marine turtles on the Togolese coast during 2012–2013. ZooKeys 779: 109-118. https://doi.org/10.3897/zookeys.779.26967
Figure 4 Distribution of marine turtle occurrences by species and location on the Togolese coast.
data and R code (including explanations) used in the preprint
<p>Contents:</p> <p>data_model_selection2.txt - used for analysing within-year variation in parasite loads via model selection and plotting Figure 1 (see R code)</p> <p>before_year_seasonal_weather2.txt - used for analysing inter-annual variation in parasite loads and plotting Figures 2-4</p> <p>Accompanying R code</p>
RSC book example dataset: Metabolomics data and R script for XCMS/R preprocessing
<p>The .zip file contains 12 (2 x 6) files from LC-MS metabolic analyses (extracts of inflorescences) of <em>Arabidopsis thaliana</em> accessions Columbia (Col-0) and Wassilewskija (Ws-3), as reported in <a href="https://doi.org/10.3389/fpls.2015.00365">https://doi.org/10.3389/fpls.2015.00365</a>, as well as an R script to analyze them with R/XCMS.</p> <p>To run the script, the directory structure of the .zip file should be kept and in R, the working directory should be set to the script directory.</p>
K-mer matrix for R-gene enrichment data of wheat Watkins diversity panel.
<p>K-mer matrix for RenSeq data of wheat lines including 300 wheat landraces from Watkins collection. The matrix is divided into 40 parts. The file “watkins_matrix_header.txt” contains the accession names and also specifies the order in which presence/absence of a k-mer is scored in the presence/absence matrix. </p>
Map 9 from: Webster R, Sweeney J, DeMerchant I (2012) New Staphylinidae (Coleoptera) records with new collection data from New Brunswick, Canada: Omaliinae, Micropeplinae, Phloeocharinae, Olisthaerinae, and Habrocerinae. ZooKeys 186: 7-29. https://doi.org/10.3897/zookeys.186.2495
Map 9 - Collection localities in New Brunswick, Canada of Olophrum rotundicolle.
Map 8 from: Webster R, Sweeney J, DeMerchant I (2012) New Staphylinidae (Coleoptera) records with new collection data from New Brunswick, Canada: Omaliinae, Micropeplinae, Phloeocharinae, Olisthaerinae, and Habrocerinae. ZooKeys 186: 7-29. https://doi.org/10.3897/zookeys.186.2495
Map 8 - Collection localities in New Brunswick, Canada of Olophrum obtectum.
Map 7 from: Webster R, Sweeney J, DeMerchant I (2012) New Staphylinidae (Coleoptera) records with new collection data from New Brunswick, Canada: Omaliinae, Micropeplinae, Phloeocharinae, Olisthaerinae, and Habrocerinae. ZooKeys 186: 7-29. https://doi.org/10.3897/zookeys.186.2495
Map 7 - Collection localities in New Brunswick, Canada of Microedus austinianus.
Map 6 from: Webster R, Sweeney J, DeMerchant I (2012) New Staphylinidae (Coleoptera) records with new collection data from New Brunswick, Canada: Omaliinae, Micropeplinae, Phloeocharinae, Olisthaerinae, and Habrocerinae. ZooKeys 186: 7-29. https://doi.org/10.3897/zookeys.186.2495
Map 6 - Collection localities in New Brunswick, Canada of Geodromicus strictus.
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.