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317 results for “R code”
SeaTemCon_R code for "The Holocene temperature conundrum answered by mollusk records from East Asia"
<p>This repository includes the code that can be used to calculate the contribution percentages of seasonal temperatures to the annual temperature for the paper entitled "The Holocene temperature conundrum answered by the mollusk records from East Asia".</p>
Data and R codes used in Delory et al (2017) F1000Research
<p>This repository contains all the data and R codes used for the use cases presented in Delory et al archiDART v3.0: a new data analysis pipeline allowing the topological analysis of plant root systems. The manuscript was submitted to F1000Research in December 2017.</p>
96 wells fluorescence reading and R code statistic for analysis
<p><strong>Overview</strong></p> <p>Data points present in this dataset were obtained following the subsequent steps: To assess the secretion efficiency of the constructs, 96 colonies from the selection plates were evaluated using the workflow presented in Figure Workflow. We picked transformed colonies and cultured in 400 μL TAP medium for 7 days in Deep-well plates (Corning Axygen®, No.: PDW500CS, Thermo Fisher Scientific Inc., Waltham, MA), covered with Breathe-Easy® (Sigma-Aldrich®). Cultivation was performed on a rotary shaker, set to 150 rpm, under constant illumination (50 μmol photons/m<sup>2</sup>s). Then 100 μL sample were transferred clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA) and fluorescence was measured using an Infinite® M200 PRO plate reader (Tecan, Männedorf, Switzerland). Fluorescence was measured at excitation 575/9 nm and emission 608/20 nm. Supernatant samples were obtained by spinning Deep-well plates at 3000 × <em>g</em> for 10 min and transferring 100 μL from each well to the clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA), followed by fluorescence measurement. To compare the constructs, R Statistic version 3.3.3 was used to perform one-way ANOVA (with Tukey's test), and to test statistical hypotheses, the significance level was set at 0.05. Graphs were generated in RStudio v1.0.136. The codes are deposit herein.</p> <p> </p> <p><strong>Info</strong></p> <p>ANOVA_Turkey_Sub.R -> code for ANOVA analysis in R statistic 3.3.3</p> <p>barplot_R.R -> code to generate bar plot in R statistic 3.3.3</p> <p>boxplotv2.R -> code to generate boxplot in R statistic 3.3.3</p> <p>pRFU_+_bk.csv -> relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>sup_+_bl.csv -> supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>sup_raw.csv -> supernatant mCherry fluorescence dataset of 96 colonies for each construct.</p> <p>who_+_bl2.csv -> whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>who_raw.csv -> whole culture mCherry fluorescence dataset of 96 colonies for each construct.</p> <p>who_+_Chlo.csv -> whole culture chlorophyll fluorescence dataset of 96 colonies for each construct.</p> <p>Anova_Output_Summary_Guide.pdf -> Explain the ANOVA files content</p> <p>ANOVA_pRFU_+_bk.doc -> ANOVA of relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>ANOVA_sup_+_bk.doc -> ANOVA of supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>ANOVA_who_+_bk.doc -> ANOVA of whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>ANOVA_Chlo.doc -> ANOVA of whole culture chlorophyll fluorescence of all constructs, plus average and standard deviation values.</p> <p> </p> <p><strong>Consider citing our work. </strong></p> <p>Molino JVD, de Carvalho JCM, Mayfield SP (2018) Comparison of secretory signal peptides for heterologous protein expression in microalgae: Expanding the secretion portfolio for Chlamydomonas reinhardtii. PLoS ONE 13(2): e0192433. https://doi.org/10.1371/journal. pone.0192433</p> <p> </p> <p> </p>
Seven Fluorescent proteins profile in Chlamydomonas reinhardtii and R code statistic for analysis
<p><strong>Overview</strong></p> <p>Data points present in this dataset were obtained following the protocol described in dx.doi.org/10.17504/protocols.io.kfnctme. We picked transformed colonies and cultured in 400 μL TAP medium for 7 days in Deep-well plates (Corning Axygen®, No.: PDW500CS, Thermo Fisher Scientific Inc., Waltham, MA), covered with Breathe-Easy® (Sigma-Aldrich®). Cultivation was performed on a rotary shaker, set to 150 rpm, under constant illumination (50 μmol photons/m<sup>2</sup>s). Then 100 μL sample were transferred clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA) and fluorescence was measured using an Infinite® M200 PRO plate reader (Tecan, Männedorf, Switzerland). Supernatant samples were obtained by spinning Deep-well plates at 3000 × <em>g</em> for 10 min and transferring 100 μL from each well to the clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA), followed by fluorescence measurement. To compare the constructs, R Statistic version 3.3.3 was used to perform one-way ANOVA (with Tukey's test), and to test statistical hypotheses, the significance level was set at 0.05. Graphs were generated in RStudio v1.0.136. The codes are deposit herein.</p> <p><strong>Info</strong></p> <p>ANOVA_Turkey_Sub.R -> code for ANOVA analysis in R statistic 3.3.3</p> <p>Anova_Output_Summary_Guide.pdf -> Explain the ANOVA files content</p> <p>Analysis_Raw_FP.xlsx -> File with raw values organized in a spreadsheet </p> <p>pRFU_<strong>FLUORESCENT PROTEIN</strong>_+_bk.csv -> relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii </em></p> <p>sup_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.csv -> supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>who_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.csv -> whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>pRFU_<strong>FLUORESCENT PROTEIN</strong>_+_bk.doc -> ANOVA of relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>sup_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.doc -> ANOVA of supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>who_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.doc -> ANOVA of whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p> </p> <p><strong>Consider citing our work. </strong></p> <p>1. Molino JVD, de Carvalho JCM, Mayfield S. Evaluation of secretion reporters to microalgae biotechnology: blue to red fluorescent proteins. Algal Res. 2018;31: 252–261. doi:10.1016/j.algal.2018.02.018</p>
Telerobotic intergroup contact: Acceptance and preferences in Israel and Palestine - R Data and code.
<p>We present telerobotics as a novel form of intergroup contact to reduce prejudice and bring about positive social change between groups in conflict. Based on our previous conceptual framework and set of design hypotheses, we conducted a survey that confronts the theory with empirical data on acceptance and preferences of the telerobotic intergroup contact approach in Israel and Palestine. The results shed light on differences in attitudes between the groups and on design considerations for telerobotics when used for intergroup contact. The study serves as a foundation for implementing this novel method of technology-enhanced conflict resolution in the field.</p> <p>The data was analyzed in R software. The archive contains the survey data and the code analyses.</p> <p> </p> <p><em>The research is supported by The Kone Foundation</em></p>
MHC_DATA and R_CODE
<p><strong>Associations among MHC genes, latitude, and haemosporidian infections in the rufous-collared sparrow (</strong><i><strong>Zonotrichia capensis</strong></i><strong>)</strong></p>
Data set for ODI cricket matches from 1987 to 2023 (extracted from ESPN Cricinfo) and code (R) used for a statistical study
<p>Here I present the data and code that has been used to study the statistical evolution of ODI cricket. The preprint for this research is available at: </p> <div> <div> <div> <table> <tbody> <tr> <td><a href="https://doi.org/10.48550/arXiv.2406.11652">https://doi.org/10.48550/arXiv.2406.11652</a> <div><span>Focus to learn more</span></div> </td> </tr> </tbody> </table> </div> </div> </div> <div> </div>
Dataset, R code and metadata for Lim et al., Pattern matters in the aposematic colouration of Papilio polytes butterflies
<p>Dataset, R code and metadata for Lim et al., Pattern matters in the aposematic colouration of Papilio polytes butterflies.</p>
Modeling data and R code for Chrysodeixis chalcites ecological niche
<p>The golden twin-spot moth, <em>Chrysodeixis chalcites</em> Esper (Lepidoptera: Noctuidae), is a polyphagous, polyvoltine crop pest occurring natively from northern Europe to Mediterranean Africa and the Canary Islands. Larvae feed on a wide variety of naturally occurring plants as well as soybean and other legume crops, short staple cotton, tomato, potato, peppers, tobacco, and banana. <em>Chrysodeixis chalcites</em> has been recorded in agricultural lands in the Ontario peninsula in eastern Canada and in northern counties of Indiana, USA. Given the strong potential for <em>C. chalcites</em> to invade USA crop lands, it is important to identify environments most likely to sustain growing populations of this pest. Though <em>C.</em> chalcites is native to Europe and North Africa, it has invaded sub-Saharan Africa. Using occurrence data form the native and invaded ranges, and environmental predictors including bioclimatic conditions and human disturbance, we trained three ecological niche models to estimate an ensemble prediction of environmental suitability in the contiguous US. Because human impact is potentially a confounding predictor, models were trained both with and without it. High environmental suitability was projected for the Atlantic coast from New England to Florida, the Gulf coast, the lower Midwest, and the Pacific coast and Central Valley of California.</p>
Assessing the Integrity of Older Archaeological Collections: An Example from La Ferrassie - supplemental material (data and R code)
<p>Supplemental data and R code for reproducing figures and table values in paper 'Assessing the Integrity of Older Archaeological Collections: An Example from La Ferrassie' by HL Dibble, SC Lin, DM Sandgathe, A Turq.</p>
R code for Rezek et al 2018 "Two million years of flaking stone ..." CORRECTION
<p>The code and the dataset for Rezek et al 2018 Two million years of flaking stone and the evolutionary efficiency of stone tool technology, Nature Ecology and Evolution. The dataset was also published with the paper doi:10.1038/s41559-018-0488-4</p>
Data and R code used in the preprint "Parasite intensity is driven by temperature in a wild bird" (doi 10.1101/323311)
<p>Data (as text files) and R code used in the preprint entitled "Parasite intensity is driven by temperature in a wild bird", recommended by <em>Peer Community In Ecology </em>(doi 10.1101/323311). See preprint and supplementary material; some explanations are also included in the R code. </p>
Data and R code associated to the publication: "Effects of land use, cover and protection on stream and riparian ecosystem services and biodiversity"
<p>This R code and dataset accompany Hanna et al's 2019 publication in Conservation Biology titled "Effects of land use, cover and protection on stream and riparian ecosystem services and biodiversity". Read the "Metadata" tab of the data file and code annotations for more information. </p>
R code and simulation output for Efford, M. G. & Boulanger, J. 2019. Fast evaluation of study designs for spatially explicit capture-recapture. Methods in Ecology and Evolution
<p>R code and simulation output for Efford, M. G. & Boulanger,<br> J. 2019. Fast evaluation of study designs for spatially explicit<br> capture-recapture. Methods in Ecology and Evolution In press.</p> <p>R code draws on previously published R packages 'secr' and 'secrdesign' available from CRAN:</p> <p><a href="https://CRAN.R-project.org/package=secr">https://CRAN.R-project.org/package=secr</a></p> <p><a href="https://CRAN.R-project.org/package=secrdesign">https://CRAN.R-project.org/package=secrdesign</a></p>
Data and R code used in Delory et al (2019) When history matters: the overlooked role of priority effects in grassland overyielding
<p>This repository contains the raw data and R code used for the following paper: Delory et al (2019) When history matters: the overlooked role of priority effects in grassland overyielding.</p>
Data and R code used in Baudson et al (2019) Developmental plasticity of Brachypodium distachyon in response to P deficiency: modulation by inoculation with phosphate-solubilizing bacteria
<p>This repository contains the raw data and R code used for the following paper: Baudson et al (2019) Developmental plasticity of <em>Brachypodium distachyon</em> in response to P deficiency: modulation by inoculation with phosphate-solubilizing bacteria</p>
R codes prepared for the manuscript, entitled "The roles of Y chromosomal genes in mouse sex spectrum phenotypes"
<p>R codes for the manuscript, entitled "The roles of Y chromosomal genes in mouse sex spectrum phenotypes" </p>
Invader defense traits in France, Japan, and the USA: dataset and R code
<p>This record includes leaf trait data for 44 species sampled in France, Japan, and the USA. R code is associated with analyses for publication.</p>
Dataset and R code for 'Do Morphometric Data Improve Phylogenetic Reconstruction? A Systematic Review and Assessment'
<p>Dataset of tree (.tre) files and R code for running generalized Robinson-Foulds distance (Smith, 2020a;b) analysis. </p> <p>The .tre files can be read into R (R Core Team., 2023) using the ape::read.tree function (Paradis et al., 2003), full details in R code file. </p> <p> </p> <p> </p> <p>Paradis, E., Claude, J., & Strimmer, K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20(2), 289-290. </p> <p>R Core Team. (2023). R: A Language and Environment for Statistical Computing. (Version 4.2.2). R Foundation for Statistical Computing, Vienna, Austria: https://www.R-project.org/. </p> <p>Smith, M. R. (2020a). Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees. Bioinformatics, 36(20), 5007-5013. https://doi.org/10.1093/bioinformatics/btaa614 </p> <p>Smith, M. R. (2020b). TreeDist: distances between phylogenetic trees. R package version 2.7.0. doi:10.5281/zenodo.3528124. </p>
Do Current Language Models Support Code Intelligence for R Programming Language?
<p>This is the dataset used in the paper: Do Current Language Models Support Code Intelligence for Programming Language?</p> <p> </p> <p>This dataset contains code snippets from R programming language repositories on GitHub, paired with their corresponding natural language (NL) descriptions. It was created for research in software engineering tasks like code summarization and code search. The data was collected using the GitHub REST API and includes over 1,500 public R repositories. To ensure quality, only active, well-structured R packages with proper documentation were included. Roxygen2, a popular documentation framework, was used to extract both the code and its matching NL descriptions.</p> <p>The dataset is organized into three parts: base R functions (Base), functions from the tidyverse (Tidy), and a combined set (RCombine). The dataset follows the CodeSearchNet format, with a split for training, validation, and testing data, ensuring no duplicate functions.</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.