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172 results for “R script”
Two-step mixed model approach to analyzing differential alternative RNA splicing: Datasets and R scripts for analysis of alternative splicing
<p>Changes in gene expression can correlate with poor disease outcomes in two ways: through changes in relative transcript levels or through alternative RNA splicing leading to changes in relative abundance of individual transcript isoforms. The objective of this research is to develop new statistical methods in detecting and analyzing both differentially expressed and spliced isoforms, which appropriately account for the dependence between isoforms and multiple testing corrections for the multi-dimensional structure of at both the gene- and isoform- level. We developed a linear mixed effects model-based approach for analyzing the complex alternative RNA splicing regulation patterns detected by whole-transcriptome RNA-sequencing technologies. This approach thoroughly characterizes and differentiates three types of genes related to alternative RNA splicing events with distinct differential expression/splicing patterns. We applied the concept of appropriately controlling for the gene-level overall false discovery rate (OFDR) in this multi-dimensional alternative RNA splicing analysis utilizing a two-step hierarchical hypothesis testing framework. In the initial screening test we identify genes that have differentially expressed or spliced isoforms; in the subsequent confirmatory testing stage we examine only the isoforms for genes that have passed the screening tests. Comparisons with other methods through application to a whole transcriptome RNA-Seq study of adenoid cystic carcinoma and extensive simulation studies have demonstrated the advantages and improved performances of our method. Our proposed method appropriately controls the gene-level OFDR, maintains statistical power, and is flexible to incorporate advanced experimental designs.</p>
Sequences, taxonomic assignments, and R script from Comparison of Lava Cave Bacterial Mat Communities to Overlying Surface Soil Bacterial Communities from Lava Beds National Monument, USA
<p>This set of files contain the 16S rDNA, taxonomic assignments from the greengenes database, and the R script for processing the data. </p> <p><strong>Abstract</strong></p> <p>Lava caves around the world often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. We generated and analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soils overlying each cave. <em>Actinobacteria</em> dominated in all samples, with 39% (caves) and 21% (surface soils). <em>Proteobacteria</em> made up 30% of phyla from caves and 36% from surface soil with <em>Gamma</em>- 20% and <em>Alpha</em>- 10% in the caves and <em>Gamma</em>- 18% with <em>Alpha</em>-17% in soil. Other major phyla in caves were <em>Nitrospirae</em> (7%) followed by Minor Phyla (7%), compared to surface soils with <em>Bacteriodetes</em> (8%) and Minor phyla (8%). A very high proportion (53.33%) of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. The same phyla were represented in both soils and cave microbial mats, but the overlap was only 11.2% at the operational taxonomic unit (OTU). Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. In terms of species richness, diversity by mat color differed, but not significantly. Number of entrances per cave, distance from an entrance, cave length, and temperature also contributed to observed differences in diversity. With high levels of novel microbes, caves may represent excellent habitats for the isolation of new bioactive compounds. This study is the first comprehensive comparisons of bacterial communities in lava caves with the overlying soil community.</p>
Database including meta data and R script for bachelor thesis biology on ground beetles as bioindicator 2017
<p>Database including meta data and R script for bachelor thesis biology on ground beetles as bioindicator 2017</p>
Patterns of Etruscan urbanism (dataset and R scripts)
<p>The present digital archive is the outcome of the paper: <strong>Stoddart, S., Palmisano, A.,Redhouse, D.I., Barker, G., di Paola, G., Motta, L., Rasmussen, T., Samuels, T., and Witcher, R., 2020. <a href="https://doi.org/10.3389/fdigh.2020.00001">Patterns of Etruscan urbanism.</a> </strong><em>Frontiers in Digital Humanities</em>, <em>7 </em>(1).<strong> </strong></p> <p>The dataset included here provides a collection of archaeological sites dating from the ninth to the fifth century BC, uncovered by systematic field survey carried out in central Italy (Tuscany and Lazio). In addition, the digital archive related to this paper provides reproducible analyses in the form of six scripts written in R statistical computing language. The present repository contains also a R Markdwon tutorial to drive step by step any practitioner interested in running some analytical tools to assess regional centralisation and settlement hierarchies: site-size histograms, rank-size graphs, A-coefficient, and B-coefficient.</p> <p> </p> <p>List of versions:</p> <ul> <li><strong>3.0 </strong>15 April 2025 - Entails revising the R scripts to replace the deprecated 'rgdal' package with the 'sf' package.</li> <li><strong>2.0.</strong> 31 March 2020 — Includes a few minor error corrections (the files 'Tutorial.RMD' and 'Tutorial.html').</li> <li><strong>1.0</strong> 31 March 2020 — First public release of the dataset on Zenodo.</li> </ul> <p> </p>
A systems analysis of sustainability impacts of agricultural policies in India - R script and supporting files
<p>This includes : </p><ul><li>two R scripts used to implement the model (residue_burning. R) and generate results (residue_burning_calls.R)</li><li>three supporting .csv files used in the R scripts above </li></ul><p> </p>
Dataset and R-scripts to the manuscript: Beyond salinity: plants show divergent responses to soil ion composition
<p>Dataset and R-scripts to the article: Pätsch R., Midolo G., Dítě Z., Dítě, D., Wagner, V., Pavonič, M., Danihelka, J., Preislerová Z., Ćuk M., Stroh H.G., Tóth T., Chytrá H., Chytrý M. (2024) Beyond salinity: plants show divergent responses to soil ion composition. <em>Global Evology and Biogeography, </em>00, e13821. <a href="https://doi.org/10.1111/geb.13821%E2%80%8B" target="_blank" rel="noopener">https://doi.org/10.1111/geb.13821</a></p>
Fallet et al - Entomopathogenic nematodes as an effective and sustainable alternative to control the fall armyworm in Africa - Dataset and R Script
<p>We tested in field trials in Rwanda in 2022 the efficacy of entomopathogenic nematodes (EPN) to control the fall armyworm (<em>Spodoptera frugiperda </em>Smith; FAW) over a complete growing season of maize. For an exhaustive description of the method, please see the publication: Fallet et al., 2024. <em>PNAS Nexus</em>. DOI: <a href="https://doi.org/10.1093/pnasnexus/pgae122">https://doi.org/10.1093/pnasnexus/pgae122</a></p> <p>Briefly, the trials were conducted in six fields each containing 20 plots. In each field, five plots were attributed to one of the following treatments (n = 30 plots per treatment in total):</p> <ul> <li>Untreated control (negative control)</li> <li>EPN formulated in a Surfactant-Polymer-Formulation (SPF; e-nema GmbH, Schwentinental, Germany)</li> <li>EPN formulated in a carboxymethyl cellulose gel (Gel; Fallet et al., 2022. Biol. Control. DOI: https://doi.org/10.1016/j.biocontrol.2022.105086</li> <li>Cypermethrin (positive control; pyrethroid contact insecticide)</li> </ul> <p>Treatments were applied into the whorl of every plant within a plot as a 2ml spot application, starting when >30% of plants were infested with FAW. Treatments were re-applied every two weeks until the maize flowers emerged. In total, treatments were applied four times in fields I, II, II and IV, and three times in fields V and VI.</p> <p><strong>Data recorded</strong></p> <ul> <li><strong>Whorl damage:</strong><br>Whorl damage was visually assessed seven- and fourteen-days post after the first-, second- and third-treatments on 40 plants per plot using the Davis whorl damage scale (Davis et al., 1992) as described in Toepfer et al. (2021). Briefly, the Davis whorl damage scale ranges from "0" to "9", whereby a fully intact whorl is attributed a score of "0", while an almost totally destroyed whorl is attributed a score of "9". Minor damages are represented by scores ranging from 1-3, while moderate or severe damages by scores ranging from 4-6 or 7-9, respectively.</li> <li><strong>FAW infestation:</strong><br>Five days after the third application of the treatments, we evaluated FAW infestation levels. For this, ten plants were destroyed in each plot to search for caterpillars. The occurrence (yes/no) of young caterpillars (shorter than 0.5 cm) was determined as a proxy for re-infestation, whereas the number of older caterpillars (longer than 0.5 cm) was used as a proxy for treatment efficacy.</li> <li><strong>Number of cobs:</strong><br>At harvest, the number of fully-developed and underdeveloped cobs from 30 plants per plot was recorded.</li> <li><strong>Cob damage:</strong><br>Fully-devloped cobs were husked to visually evaluate cob damage, using a "0" to "3" customized damage score, where "0" represents an intact cob, while scores of "1", "2", or "3" represent minor (<5% damaged kernels), moderate (5-20% damaged kernels) or severe (>20% damaged kernels) cob damage, respectively.</li> <li><strong>Yield:</strong><br>The husked cobs from 30 plants were weighed together to estimate fresh weight (FW) yield per plot.</li> </ul> <p> </p> <p> </p>
finnpiatscheck/Environmental-Effects-on-a-Fig-Wasp-Community: Data sets and R scripts
<p>These are the data and R scripts used in the paper "Landscape-Level Analysis of a Fig-Pollinator-Antagonist Community: Spatial and Temporal Variation in a Fig Wasp Community and its Response to Biotic and Abiotic Factors".</p>
R scripts for "Using LiDAR to assess the influence of fine-scale habitat structure on the abundance of the bearded reedling (Panurus biarmicus)"
<p>Dataset which contains R scripts and R package SDMaps used for data preparation and modelling in the methodology described in my MSc thesis "Using LiDAR to assess the influence of fine-scale habitat structure on the abundance of the bearded reedling (<em>Panurus biarmicus</em>)".</p> <p>The project involved creating Species Distribution Models to test whether and how fine-scale habitat structure - in the form of LiDAR derived variable - influences the relative abundance of the bearded reedling in the Netherlands, beyond other variables such as land use, soil type and climate data.</p> <p>These scripts can serve as an example of how the SDMaps package can be used to build Species Distribution Models that include LiDAR derived variables, and to replicate some of the methodologies described in the thesis. The SDMaps package contains an installation guide, manual, tutorial and examples.</p>
Data and R script for "Fear and cultural background drive sexual prejudice in France – A sentiment analysis approach"
<p>Data:</p> <p>corpus_integral.csv</p> <p>FEEL_1.csv</p> <p>mauvais.txt</p> <p>neg_hetero_corrected.txt</p> <p>participant_info_used.txt</p> <p>pos_hetero_corrected.txt</p> <p>R script:</p> <p>polarities.R</p> <p>sentiments_discrete.R</p>
Mimulus cardinalis plasticity analyses and R scripts for: Spatial variation in high temperature-regulated gene expression predicts evolution of plasticity with climate change in the scarlet monkeyflower
<p>A major way that organisms can adapt to changing environmental conditions is by evolving increased or decreased phenotypic plasticity. In the face of current global warming, more attention is being paid to the role of plasticity in maintaining fitness as abiotic conditions change over time. However, given that temporal data can be challenging to acquire, a major question is whether evolution in plasticity across space can predict adaptive plasticity across time. In growth chambers simulating two thermal regimes, we generated transcriptome data for western North American scarlet monkeyflowers (<i>Mimulus cardinalis</i>) collected from different latitudes and years (2010 and 2017) to test hypotheses about how plasticity in gene expression is responding to increases in temperature, and if this pattern is consistent across time and space. Supporting the genetic compensation hypothesis, individuals whose progenitors were collected from the warmer-origin northern 2017 descendant cohort showed lower thermal plasticity in gene expression than their cooler-origin northern 2010 ancestors. This was largely due to a change in response at the warmer (40ºC) rather than cooler (20ºC) treatment. A similar pattern of reduced plasticity, largely due to a change in response at 40ºC, was also found for the cooler-origin northern versus the warmer-origin southern population from 2017. Our results demonstrate that reduced phenotypic plasticity can evolve with warming and that spatial and temporal changes in plasticity predict one another.</p>
Coded data and R scripts for the article-Toward a dynamic behavioral profile of the Mandarin Chinese temperature term re
<p>These are the coded dataset and R scripts for the article "Towards a dynamic behavioral profile of Mandarin Chinese temperature term re: A diachronic semasiological approach".</p>
R script with data for vegetation and macropod scat analysis
<p>Fire and herbivores alter vegetation structure and function. Future fire activity is predicted to increase, and quantifying changes in vegetation communities arising from post-fire herbivory is needed to better manage natural environments.</p> <p>We investigated the effects of post-fire herbivory on understory plant communities in a coastal eucalypt forest in south-eastern Australia. We quantified herbivore activity, understory plant diversity, and dominant plant morphology following a wildfire in 2017 using two sizes of exclosures. Statistical analysis incorporated the effect of exclusion treatments, time since fire (TSF), and the effect of a previous prescribed burn.</p> <p>Exclusion treatments altered herbivore activity, but TSF did not. Herbivory reduced plant species richness, diversity and evenness and promoted the dominance of the most abundant plants within the understory. Increasing TSF reduced community diversity and evenness and influenced morphological changes to the dominant understory plant species, increasing size and dead material while decreasing abundance. We found the legacy effects of a previous prescribed burn had no effect on herbivores or vegetation within our study.</p> <p>Foraging by large herbivores resulted in a depauperate vegetation community. As post-fire herbivory can alter vegetation communities, we postulate that management burning practices may exacerbate herbivore impacts.</p> <p>Future fire management strategies to minimise herbivore-mediated alterations to understory vegetation could include aggregating management burns into larger fire sizes or linking fire management with herbivore management. Restricting herbivore access following fire (planned or otherwise) can encourage a more diverse and species-rich understory plant community. Future research should aim to determine how vegetation change from post-fire herbivory contributes to future fire risk.</p>
Dataset and R script for Collection and Processing of Behavioural Data of the Olive Fruit Fly, Bactrocera oleae, when Exposed to Olive Twigs Treated with Different Commercial Products
<p>We provide raw data and R script for analysis of data published in:</p> <p>1) Daher, E.; Cinosi, N.; Chierici, E.; Rondoni, G.; Famiani, F.; Conti, E. Field and Laboratory Efficacy of Low-Impact Commercial<br> Products in Preventing Olive Fruit Fly, Bactrocera oleae, Infestation. Insects 2022, 13, 213. https://doi.org/10.3390/insects13020213</p> <p>2) Daher, E.; Chierici, E.; Cinosi, N.; Rondoni, G.; Famiani, F.; Conti, E. Collection and Processing of Behavioural Data of the Olive Fruit Fly, <em>Bactrocera oleae</em>, when Exposed to Olive Twigs Treated with Different Commercial Products. <em>Data </em><strong>2022</strong>, <em>7</em>,</p>
Occurrence datasets, model outputs, and R script for 12 termite species used for niche modeling
<p>The advent of citizen-science databases in conjunction with museum specimen locality information has exponentially increased the power and accuracy of ecological niche modeling (ENM). Increased occurrence data has provided colossal potential to understand the distributions of lesser known or endangered species, including arthropods. Although niche modeling of termites has been conducted in the context of invasive and pest species, few studies have been performed to understand the distribution of basal termite genera. Using specimen records from the American Museum of Natural History (AMNH) as well as locality databases, we generated ecological niche models for 12 basal termite species belonging to six genera and three families. We extracted environmental data from the Worldclim 19 bioclimatic dataset v2, along with SoilGrids datasets and generated models using MaxEnt. We chose Optimal models based on partial Receiving Operating characteristic (pROC) and omission rate criterion and determined variable importance using permutation analysis. We also calculated response curves to understand changes in suitability with changes in environmental variables. Optimal models for our 12 termite species ranged in complexity, but no discernible pattern was noted among genera, families, or geographic range. Permutation analysis revealed that habitat suitability is affected predominantly by seasonal or monthly temperature and precipitation variation. Our findings not only highlight the efficacy of largely citizen-science and museum-based datasets, but our models provide a baseline for predictions of future abundance of lesser-known arthropod species in the face of habitat destruction and climate change.</p>
Data and R scripts for: Identifying existing management practices in the control of Striga asiatica within rice–maize systems in mid-west Madagascar
<p>Infestations by the parasitic weed genus <i>Striga</i> result in significant losses to cereal crop yields across sub-Saharan Africa. The problem disproportionately affects subsistence farmers who frequently lack access to novel technologies. Effective <i>Striga </i>management therefore requires the development of strategies utilising existing cultural management practices. We report a multi-year, landscape-scale monitoring project for <i>Striga</i> asiatica in the mid-west of Madagascar, undertaken over 2019-2020 with the aims of examining cultural, climatic and edaphic factors currently driving abundance and distribution. Long-distance transects were established across the middle-west region of Madagascar, over which <i>Striga asiatica</i> abundance in fields was estimated. Analysis of the data highlights the importance of crop variety and legumes in driving <i>Striga </i>density. Moreover, the dataset revealed significant effect of precipitation seasonality, mean temperature and altitude in determining abundance. A composite management index indicated the effect of a range of cultural practices on changes in <i>Striga </i>abundance<i>. </i>The findings support the assertion that single measures are not sufficient for the effective, long-term management of <i>Striga</i>. Furthermore, the composite score has potential as a significant guide of integrated <i>Striga </i>management beyond the geographic range of this study. </p>
Data and R script: Ecotourism impacts on reef fishes in a marine reserve during the COVID-19 era
<p>Raw data and R code necessary to reproduce the results of the paper entitled "Ecotourism impacts on reef fishes in a marine reserve during the COVID-19 era" published in Frontiers in Ecology and the Environment.</p> <p> </p>
Segmentation performance evaluation results and R scripts for generating figures and tables.
<p>This archive contains the evalutation results of 24 segmentation models and the R scripts to produce figures and tables published in Kloster et al. 2022: Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint.</p> <p>Please refer to the manuscript for further details.</p>
R-Script surface contour: Republic of Moldova project report Free University Berlin
<p>This R-Script supplements (surface contour) the project of the Freie Universität Berlin with the title: <strong>Anwendung geoarchäoogischer Methoden zum Verständnis anthropogener Spuren der Poineşti-Lucaşeuca Kultur in Ivancea-Sub Pădure, Republik Moldau. </strong>The project was carried out by students during the module Projekt I at the Freien Universität Berlin. Fieldwork was conducted 16th - 23rd September 2018in the vicinity of Ivancea (central Moldova), about 30km north of the capital Chisinau. </p>
Post-revision data and R Script for Murtagh et al. 'The scent of enrichment: Exploring the effect of odour and biological salience on behaviour during enrichment of kennelled dogs.'
<p>Data and analysis file (written in R studio) for the paper Murtagh et al. 'The scent of enrichment: Exploring the effect of odour and biological salience on behaviour during enrichment of kennelled dogs.' Updated based on reviewer comments and additional analyses requested (master data and analysis filed labelled with 'rev' suffix).</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.