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Dataset results
16 results for “independence sampling”
Linkage-independent SNPs in the Drosophila melanogaster Sussex LHM sample
<p>Unix code for running Plink program for generating a list of SNPs (single-nucleotide polymorphisms) which are independent of linkage diseqiulibrium. Used for later statistical analyses incorporating the number of independent tests made across the genome.</p>
Text-fig. 13. Scatter diagram of m1 length vs SDQ for pre-Eemian (time slice 5) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 13. Scatter diagram of m1 length vs SDQ for pre-Eemian (time slice 5) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain.
Text-fig. 11. Scatter diagram of m1 length vs SDQ for Würmian/Weichselian (time slice 3) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and extant Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 11. Scatter diagram of m1 length vs SDQ for Würmian/Weichselian (time slice 3) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and extant Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain.
Text-fig. 12. Scatter diagram of m1 length vs SDQ for Eemian (time slice 4) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 12. Scatter diagram of m1 length vs SDQ for Eemian (time slice 4) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain.
Text-fig. 10. Scatter diagram of m1 length vs SDQ for Extant (time slice 1 and 2) Arvicola samples of different geographical provenances compared with M. savini-A. mosbachensis. Abbreviations: EU – Europe, GE – Germany, IT – Italy, SP – Spain. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 10. Scatter diagram of m1 length vs SDQ for Extant (time slice 1 and 2) Arvicola samples of different geographical provenances compared with M. savini-A. mosbachensis. Abbreviations: EU – Europe, GE – Germany, IT – Italy, SP – Spain.
Text-fig. 1. SDQ vs stratigraphic time in samples of Mimomys savini and Arvicola from various Italian and German localities (in brackets: sample size), showing a parallel trend starting from ca. 200 ka. From Maul et al. (1998b: fig. 4), modified. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 1. SDQ vs stratigraphic time in samples of Mimomys savini and Arvicola from various Italian and German localities (in brackets: sample size), showing a parallel trend starting from ca. 200 ka. From Maul et al. (1998b: fig. 4), modified.
Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex
Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree and rate of plastome degradation in a complex of leafless orchids (Corallorhiza striata) across its geographic range. Plastomes provide strong support for relationships and evidence of reciprocal monophyly between C. involuta and the endangered C. bentleyi. Plastome degradation is extensive, occurring rapidly over a few million years, with evidence of differing rates of substitution among the two principal clades of the complex. Genome skimming and targeted sequence capture differ widely in coverage depth overall, with depth in targeted sequence capture datasets varying immensely across the plastome as a function of GC content. These findings will help fill a knowledge gap in models of heterotrophic plastid genome evolution, and have implications for future studies in heterotrophs.
Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex
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Micron-resolution fiber mapping in histology independent of sample preparation
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Data from: An efficient independence sampler for updating branches in Bayesian Markov chain Monte Carlo sampling of phylogenetic trees
Sampling tree space is the most challenging aspect of Bayesian phylogenetic inference. The sheer number of alternative topologies is problematic by itself. In addition, the complex dependency between branch lengths and topology increases the difficulty of moving efficiently among topologies. Current tree proposals are fast but sample new trees using primitive transformations or re-mappings of old branch lengths. This reduces acceptance rates and presumably slows down convergence and mixing. Here, we explore branch proposals that do not rely on old branch lengths but instead are based on approximations of the conditional posterior. Using a diverse set of empirical data sets, we show that most conditional branch posteriors can be accurately approximated via a Γ distribution. We empirically determine the relationship between the logarithmic conditional posterior density, its derivatives, and the characteristics of the branch posterior. We use these relationships to derive an independence sampler for proposing branches with an acceptance ratio of ∼90% on most data sets. This proposal samples branches between 2× and 3× more efficiently than traditional proposals with respect to the effective sample size per unit of runtime. We also compare the performance of standard topology proposals with hybrid proposals that use the new independence sampler to update those branches that are most affected by the topological change. Our results show that hybrid proposals can sometimes noticeably decrease the number of generations necessary for topological convergence. Inconsistent performance gains indicate that branch updates are not the limiting factor in improving topological convergence for the currently employed set of proposals. However, our independence sampler might be essential for the construction of novel tree proposals that apply more radical topology changes.
Data from: An efficient independence sampler for updating branches in Bayesian Markov chain Monte Carlo sampling of phylogenetic trees
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Purity Independent Subtyping of Tumors (PurIST), a clinically robust single-sample classifier for tumor subtyping in pancreatic cancer (RNA-Seq)
GEO Series GSE131050. Homo sapiens. 191 samples. Type: Expression profiling by high throughput sequencing.
microRNA expression profile of human thymus populations corresponding to 8 sequential T-cell developmental stages isolated from 3 independent pediatric thymus samples.
GEO Series GSE299842. Homo sapiens. 23 samples. Type: Non-coding RNA profiling by array.
Purity Independent Subtyping of Tumors (PurIST), a clinically robust single sample classifier for tumor subtyping in pancreatic cancer (NanoString)
GEO Series GSE131051. Homo sapiens. 58 samples. Type: Expression profiling by array.
Purity Independent Subtyping of Tumors (PurIST), a clinically robust single sample classifier for tumor subtyping in pancreatic cancer
GEO Series GSE131049. Homo sapiens. 249 samples. Type: Expression profiling by array; Expression profiling by high throughput sequencing.
Affymetrix SNP6 array data for ACTH-Independent Macronodular Adrenal Hyperplasia (AIMAH) samples
GEO Series GSE42171. Homo sapiens. 52 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
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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.