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ShareScore release 0.9.0
Dataset results
6 results for “concatenated analysis”
Data from: The complex effects of demographic history on the estimation of substitution rate: concatenated gene analysis results in no more than twofold overestimation
Our recent estimation of the divergence time and isolation of Death Valley pupfishes, including the iconic Devil's Hole pupfish (DHP), rewrote widespread assumptions about this group. These species were previously assumed to be relic populations isolated over millions of years; our genomic analyses indicated recent colonization of Devil's Hole within the past 105–830 years and frequent gene flow among Death Valley populations [1]. These results understandably attracted substantial attention given the iconic battle for conservation and intense management of DHP [2]; nonetheless, a young age for this species should not diminish its conservation value. Indeed, we argue that the unique natural history of this species makes it a prime candidate for exhibiting one of the fastest mutation rates observed in any vertebrate [3].
Root images for testing concatenation and statistical analysis with RhizoVision Explorer
<p>Thresholded images of cleaned and scanned roots as described for a paper entitled:</p> <p>"Divide and conquer: Using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods"</p> <p>The zip file contains two main folders for Original and Concatenated images. Each contains a subfolder for the 3 different image sets for switchgrass, poplar, and petaland (which also includes some arctic samples). Original images include multiple scans of the same sample where the sample is denoted as a letter. Concatenated images were generated in python combining multiple scans of the same sample into one large image based on the common letter.</p>
Data from: The complex effects of demographic history on the estimation of substitution rate: concatenated gene analysis results in no more than twofold overestimation
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Data from: Incomplete lineage sorting impacts the inference of macroevolutionary regimes from molecular phylogenies when concatenation is employed: an analysis based on Cetacea
Interest in methods that estimate speciation and extinction rates from molecular phylogenies has increased over the last decade. The application of such methods requires reliable estimates of tree topology and node ages, which are frequently obtained using standard phylogenetic inference combining concatenated loci and molecular dating. However, this practice disregards population-level processes that generate gene tree/species tree discordance. We evaluated the impact of employing concatenation and coalescent-based phylogeny inference in recovering the correct macroevolutionary regime using simulated data based on the well-established diversification rate shift of delphinids in Cetacea. We found that under scenarios of strong incomplete lineage sorting, macroevolutionary analysis of phylogenies inferred by concatenating loci failed to recover the delphinid diversification shift, while the coalescent-based tree consistently retrieved the correct rate regime. We suggest that ignoring microevolutionary processes reduces the power of methods that estimate macroevolutionary regimes from molecular data.
Data from: Incomplete lineage sorting impacts the inference of macroevolutionary regimes from molecular phylogenies when concatenation is employed: an analysis based on Cetacea
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Data from: When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny
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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.