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580 results for “pattern analysis”
Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis
<p>Raw data set for npj Bioflims and Microbiome article: “Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis”</p>
Analysis of rod-cone dystrophy genes reveals unique mutational patterns
<div> Background <p>Rod-cone dystrophy (RCD) is the most common inherited retinal disease that is characterised by the progressive degeneration of retinal photoreceptors. RCD genes' classification is based exclusively on gene mutations' prevalence and does not consider the implication of the same gene in different phenotypes. Therefore, we first investigated the mutations occurrence in autosomal recessive RCD (arRCD) and non-arRCD conditions. Then, finally, we identified arRCD enriched mutational patterns in specific genes and coding exons<strong>.</strong></p> </div> Methods and results <p>The mutations' patterns differed according to arRCD (p=0.001). Specifically, When compared with missense; insertions/deletions (OR=1.2, p=0.007), nonsense (OR=1.2, p=0.014) and splice-site mutations (OR=1.6, p=0.038) increased the OR of arRCD by 20%–60% versus non-arRCD conditions. The gene-based analysis identified that EYS, IMPG2, RP1L1 and USH2A mutations were enriched in arRCD (p<0.05). The exon-based analysis revealed specific mutation patterns in exons of CRB1, RP1L1 and exons 12, 60 and 62 coding for Lamin EGF and FTIII domains of USH2A.</p> <p></p> <div> Conclusion <p>The current analysis showed that many aRCD genes have unique mutational patterns.</p> </div>
Original data for "Unsupervised Analysis of Optical Imaging Data for the Discovery of Reactivity Patterns in Metal Alloy" article
<p>This upload includes both original and supplementary data for the publication "Unsupervised Analysis of Optical Imaging Data for the Discovery of Reactivity Patterns in Metal Alloy" by R. Li, A. Makogon, T. Galochkina, J-F. Lemineur, F. Kanoufi, and V. Shkirskiy, published in the Small Methods journal. The preprint version of the paper is available on ChemRxiv (<a href="https://doi.org/10.26434/chemrxiv-2023-sgvt0">https://doi.org/10.26434/chemrxiv-2023-sgvt0</a>).</p> <p>The file "Data_processing.zip" contains the original optical image of the interface, maps of film evolution rates in acidic and salt environments, COMSOL data output in acidic and salt environments, as well as a Jupyter Lab file that demonstrates how to process this data.</p> <p>The file "Comparison_of_SEM_images.zip" includes the original SEM images used in the current study and in our previous work (<a href="https://doi.org/10.26434/chemrxiv-2022-rn77b-v3">https://doi.org/10.26434/chemrxiv-2022-rn77b-v3</a>), along with a Jupyter Lab file that illustrates the data processing procedure.</p> <p>The file "Original_data_in_npy_format.zip" contains all original data from SEM/EDX and RM experiments.</p> <p>We recommend opening the Jupyter Lab files in a Python 3 environment. PDF files in the root directory provide outputs of all uploaded Jupyter Lab files.</p>
Dataset for: Fifty years of research on questionable research practices in science: Quantitative analysis of co-citation patterns
<p>Questionable research practices (QRPs) have been the focus of the scientific community amid greater scrutiny and evidence highlighting issues with replicability across many fields of science. To capture the most impactful publications and the main thematic domains in the literature on QRPs, this study uses a document co-citation analysis. The analysis was conducted on a sample of 341 documents that covered the past 50 years of research in QRPs. Nine major thematic clusters emerged. Statistical reporting and statistical power emerged as key areas of research, where systemic-level factors in how research is conducted are consistently raised as the precipitating factors for QRPs. There is also an encouraging shift in the focus of research into open science practices designed to address engagement in QRPs. Such a shift is indicative of the growing momentum of the open science movement, and more research can be conducted on how these practices are employed on the ground and how their uptake by researchers can be further promoted. However, the results suggest that, while pre-registration and registered reports receive the most research interest, less attention has been paid to other open science practices (e.g., data and methods sharing).</p>
Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes
<p>Dataset used to reproduce the analysis performed in "Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes" publication. The directory structure is the following:</p> <ul> <li>Gene_models - directory containing gene models (.gtf or .gff3 files) used for feature length comparisons across species</li> <li>intermediate_data - directory containing intermediate results from various scripts, the main purpose is to speed up the reproducibility of some longer running scripts <ul> <li>batch_adjusted_normalised_gene_expression_matrix.tsv - gene expression matrix used for evolutionary model fitting</li> <li>fc.tsv - fold change matrix used for evolutionary model fitting</li> <li>dated_species_tree.tre - species tree used throughout the model fitting step (newick format)</li> <li>DGE_script_enviorment.RData - saved R environment from differential gene expression analysis</li> <li>downregulated_IDs.RDS - gene IDs which undergo down-regulation throughout maternal-to-zygotic transition</li> <li>maternal_IDs.RDS - gene IDs which meet the cut-off criteria for being considered as maternally expressed</li> <li>N0_blasted.tsv - orthogroup annotations through blasting to a sequence database</li> <li>N0.tsv - orthogroups inferred from OrthoFinder</li> <li>OG_categories.tsv - classification of orthogroups based on them (I) having genes with maternal expression, but no significant down regulation, (II) having genes with maternal expression and significant down regulation throughout maternal-to-zygotic transition or (III) no maternal expression</li> <li>OG_presence.tsv - binary matrix coding for which orthogroup which species have gene expression values</li> <li>Paralog_variances.tsv - matrix containing variance metrics for paralogs in each species from before normalization across species</li> </ul> </li> <li>Pannzer2_annotation - directory containing GO annotations for all species from the Pannzer2 tool, used for GO analyses</li> <li>quantification_files - directory containing all salmon quantification outputs</li> <li>transcriptomes - <em>de novo</em> assembled transcriptomes for non-model species</li> </ul>
Real-World Analysis of Belantamab Mafodotin Care Patterns in Patients With Relapsed and/or Refractory Multiple Myeloma
ClinicalTrials.gov study NCT05986682. IPD Sharing: NO. Countries: 1. Publications: 1.
Treatment Patterns With Targeted Therapies In Mrcc In Sweden - A Retrospective Analysis Of Data From National Registries
ClinicalTrials.gov study NCT04669366. IPD Sharing: NO. Countries: 1. Publications: 1.
Meta-analysis of the Portfolio Dietary Pattern and Cardiometabolic Risk
ClinicalTrials.gov study NCT03534414. IPD Sharing: NO. Countries: 1. Publications: 5.
Data from: Diversity and plasticity in mosquito feeding patterns: a meta-analysis of ‘universal’ DNA diet studies
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Dataset for: Fifty years of research on questionable research practices in science: Quantitative analysis of co-citation patterns
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Data from: Evolution of plumage patterns in pattern morphospace: A phylogenetic analysis of melanerpine woodpeckers
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Temporal and spatial pattern analysis of escaped prescribed fires in California from 1991 to 2020
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Analysis of temporal patterns in animal movement networks
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Analysis of rod-cone dystrophy genes reveals unique mutational patterns
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Data from: Computed tomographic analysis of dental system of three Jurassic ceratopsians: implications for the evolution of the tooth replacement pattern and diet in early-diverging ceratopsians
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Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow
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Data from: A new digital method of data collection for spatial point pattern analysis in grassland communities
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Data from: Beta diversity patterns of bats in the Atlantic Forest: how does the scale of analysis affect the importance of spatial and environmental factors?
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Data from: Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination
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Short-Tandem-Repeat (STR) marker set for Eurasian lynx for article: Genetic analysis indicates spatial-dependent patterns of sex-biased dispersal in Eurasian lynx in Finland
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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.