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100 results for “genetic code”
Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history
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Stan code from: Simulation modeling reveals the evolutionary role of landscape shape and species dispersal on genetic variation within a metapopulation
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Data and code from: Landscape-driven isolation among, but high genetic diversity within, peripheral populations of a threatened frog
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Stan code from: Branching networks can have opposing influences on genetic variation in riverine metapopulations
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Data and Code for Publication "Testing the Utility of Dental Morphological Trait Combinations for Inferring Human Neutral Genetic Variation"
<p>Data and code for publication: H. Rathmann, H. Reyes-Centeno, Testing the utility of dental morphological trait combinations for inferring human neutral genetic variation. <em>Proc. Natl. Acad. Sci. U.S.A.</em> 117, 10769-10777 (2020). DOI: 10.1073/pnas.1914330117</p> <p>The repository contains:</p> <ul> <li>“R-code.txt”: R code for an exhaustive search algorithm testing the utility of dental morphological traits and trait combinations for inferring human neutral genetic variation.</li> <li>“dental trait frequencies.csv”: Data set with 27 dental morphological trait frequencies for 20 modern human populations worldwide used for analysis. Data from G. R. Scott, C. G. Turner, G. C. Townsend, M. Martinón-Torres, <em>The Anthropology of Modern Human Teeth</em> (Cambridge University Press, 2018). DOI: 10.1017/ 9781316795859</li> <li>“microsatellite loci mean sizes.csv”: Data set with 645 microsatellite mean allele sizes for 20 modern human populations worldwide used for analysis. Data from T. J. Pemberton, M. DeGiorgio, N. A. Rosenberg, Population structure in a comprehensive genomic data set on human microsatellite variation. <em>G3: Genes Genom. Genet.</em> 3, 891–907 (2013). DOI: 10.1534/g3.113.005728</li> <li>“utility estimates for 134217727 trait combinations.txt”: A large table with utility estimates for 27 dental morphological traits and all 134,217,700 possible trait combinations.</li> </ul> <p>Abbreviations for the 20 population names (rows) in “dental trait frequencies.csv” and “microsatellite loci mean sizes.csv” as follows:</p> <ul> <li>AUS = Australia</li> <li>CAS = Central Asia</li> <li>EAF = Eastern Africa</li> <li>EAS = East Asia</li> <li>EEU = Eastern Europe</li> <li>IND = India</li> <li>MAM = Mesoamerica</li> <li>MEL = Melanesia</li> <li>MIC = Micronesia</li> <li>NAF = North Africa</li> <li>NAM = North America</li> <li>NESI = Northeast Siberia</li> <li>NGU = New Guinea</li> <li>NWAM = Na-Dene</li> <li>POL = Polynesia</li> <li>SAM = South America</li> <li>SAN = San</li> <li>SEAS = Southeast Asia</li> <li>WEU = Western Europe</li> <li>WSAF = Sub-Saharan Africa</li> </ul> <p>Abbreviations for the 27 dental morphological trait names (columns) in “dental trait frequencies.csv” as follows:</p> <ul> <li>T1 = Winging (UI1)</li> <li>T2 = Shoveling (UI1)</li> <li>T3 = Double-Shoveling (UI1)</li> <li>T4 = Interruption Grooves (UI2)</li> <li>T5 = Tuberculum Dentale (UI2)</li> <li>T6 = Mesial Ridge (UC)</li> <li>T7 = Distal Accessory Ridge (UC)</li> <li>T8 = Hypocone (UM2)</li> <li>T9 = Carabelli Trait (UM1)</li> <li>T10 = Cusp 5 (UM1)</li> <li>T11 = Enamel Extensions (UM1)</li> <li>T12 = Peg-Reduced-Missing (UM3)</li> <li>T13 = Lingual Cusp Number (LP2)</li> <li>T14 = Groove Pattern (LM2)</li> <li>T15 = Cusp 6 (LM1)</li> <li>T16 = Cusp Number (LM2)</li> <li>T17 = Deflecting Wrinkle (LM1)</li> <li>T18 = Distal Trigonid Crest (LM1)</li> <li>T19 = Protostylid (LM1)</li> <li>T20 = Cusp 7 (LM1)</li> <li>T21 = Odontomes (UP-LP)</li> <li>T22 = Root Number (UP1)</li> <li>T23 = Root Number (UM2)</li> <li>T24 = Root Number (LC)</li> <li>T25 = Tomes’ Root (LP1)</li> <li>T26 = Root Number (LM1)</li> <li>T27 = Root Number (LM2)</li> </ul> <p>Abbreviations for the 645 microsatellite allele locus names (columns) in “microsatellite loci mean sizes.csv” as in T. J. Pemberton, M. DeGiorgio, N. A. Rosenberg, Population structure in a comprehensive genomic data set on human microsatellite variation. <em>G3: Genes Genom. Genet.</em> 3, 891–907 (2013). DOI: 10.1534/g3.113.005728</p>
Abundant genetic variation is retained in many laboratory schistosome populations - Code and data
<p>Code and data used for the generation of figures in manuscript.</p>
Evolution of the Genetic Code in Phyllopharyngean Ciliates
<p>Multiple Independent Genetic Code Reassignments of the UAG Stop Codon in Phyllopharyngean Ciliates.</p> <p> </p> <p>Genome assemblies and annotations of 10 Phyllopharyngean ciliates.</p> <p>The three TARA Oceans Ciliate MAGs were downloaded from https://www.genoscope.cns.fr/tara/.</p> <p>Assemblies for the other seven species were de novo assembled from reads downloaded from the BioProjects PRJNA413041 and PRJNA546036.</p> <p> </p>
Supporting code and data for: Exploring the role of asexual multiplication in poplar rust epidemics: impact on diversity and genetic structure
<p>This is the first release of the updated code for the analyses of the related article published in Molecular Ecology.</p>
Code from: Realistic genetic architecture enables organismal adaptation as predicted under the folk definition of inclusive fitness
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Genetic code expansion in stable cell lines enables encoded chromatin modification
GEO Series GSE73823. Mus musculus. 40 samples. Type: Expression profiling by high throughput sequencing.
Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [RNA-seq]
GEO Series GSE185908. Homo sapiens. 120 samples. Type: Expression profiling by high throughput sequencing.
Multi-omic Analysis of Developing Human Retina and Organoids Reveals Cell-Specific Cis-Regulatory Elements and Mechanisms of Non-Coding Genetic Disease Risk.
GEO Series GSE183684. Homo sapiens. 51 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [STARR-seq]
GEO Series GSE185939. Homo sapiens. 16 samples. Type: Other.
Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases
GEO Series GSE185941. Homo sapiens. 146 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Dissecting the Genetics of the Human Transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci
GEO Series GSE65907. Homo sapiens. 2112 samples. Type: Expression profiling by array.
Massively parallel quantification of the regulatory effects of non-coding genetic variation
GEO Series GSE68331. Homo sapiens. 8 samples. Type: Other.
The Genetic Architecture of Congenital Diarrhea and Enteropathy (CODE)
GEO Series GSE264461. Danio rerio. 4 samples. Type: Expression profiling by high throughput sequencing.
Deciphering a secondary genetic code in neurons: the role of codon bias in regulating neuronal protein levels and implications for Elongator-mediated neurological disease
GEO Series GSE80130. Mus musculus. 8 samples. Type: Expression profiling by array.
Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [ChIP-seq]
GEO Series GSE185928. Homo sapiens. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Non-coding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation
GEO Series GSE145997. Homo sapiens. 74 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
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.