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Dataset results
349 results for “Comparative methods”
Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (Drop-Seq)
GEO Series GSE118706. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods
GEO Series GSE142286. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (Cel_Seq)
GEO Series GSE118704. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Comprehensive comparative analysis of 5’ end RNA sequencing methods
GEO Series GSE103486. Homo sapiens. 19 samples. Type: Expression profiling by high throughput sequencing; Other.
Comparative analysis of single-cell RNA sequencing methods
GEO Series GSE75790. Mus musculus. 583 samples. Type: Expression profiling by high throughput sequencing; Third-party reanalysis.
Systematic comparative analysis of strand-specific, cost-effective, RNA-seq library preparation methods for low input samples
GEO Series GSE167300. Homo sapiens. 50 samples. Type: Other.
Gene Expression Profiling of Whole Blood: A Comparative Assessment of RNA-Stabilizing Collection Methods
GEO Series GSE103889. Homo sapiens. 64 samples. Type: Expression profiling by array.
Comparing Reference-Based RNA-Seq Mapping Methods for Non-Human Primate Data
GEO Series GSE57485. Papio cynocephalus. 12 samples. Type: Expression profiling by high throughput sequencing.
Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (9 cell mixture dataset).
GEO Series GSE117450. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
Comparative Analysis of Methods to Reduce Activation Signature Gene Expression in PBMCs
GEO Series GSE236732. Homo sapiens. 25 samples. Type: Expression profiling by high throughput sequencing.
singIST: an integrative method for comparative single-cell transcriptomics between disease models and humans
GEO Series GSE314373. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
High-dimensional transcriptional analyses of UC Colon comparing RNALater to DMSO collection method
GEO Series GSE108746. Homo sapiens. 72 samples. Type: Expression profiling by high throughput sequencing.
Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods [5 Cell Lines Cel-seq]
GEO Series GSE126908. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (RNAmix_Sort-seq)
GEO Series GSE117618. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Assessment of real-time PCR for Helicobacter pylori DNA detection in stool with co-infection of intestinal parasites: a comparative study of DNA extraction methods
<p>Background</p> <p>Many studies reported high prevalence of <em>H. pylori</em> infection among patients co-infected with intestinal parasites. Molecular approach for the DNA detection of those microbes in stool have been proposed. However there are a few reports that evaluated the effect of bead-beating in relation to the <em>H. pylori</em> outcome. Therefore, we developed and evaluated two TaqMan-based real-time PCR (rt-PCR) qualitative assays for the detection of <em>ureC</em> (<em>glmM</em>) and <em>cagA</em> of <em>Helicobacter pylori</em> on DNA extracted by three procedures.</p> <p>Results</p> <p>The two PCRs were analysed on 100 stool samples from patients who were screened for intestinal parasites. Three DNA extraction procedures were used: 1) automation with bead beating, 2) automation without bead beating and 3) hand column. The specificity of the new assays was confirmed by sequencing the PCR products and by the lack of cross-reactivity with other bacteria or pathogens DNA. Rt-PCR assays showed a detection limit of 10^4 bacteria/200 mg stool. The <em>ureC</em>_PCR with bead beating process was compared to conventional stool antigen test (SAT), with 94.12 and 93.75% of respectively sensitivity and specificity. However, the discordant samples were confirmed by DNA sequencing suggesting a potential higher sensitivity and specificity of PCR.</p> <p>Conclusions</p> <p>Our findings showed that the automation with bead-beating –suggested procedure for intestinal parasitic infections- can reach highly sensitive results in <em>H. pylori</em> detection on stool compared also with SAT. Thus, this work can provide new insights into the practice of a clinical microbiology laboratory in order to optimize detection of gastro-intestinal infections. Further studies are needed to better define the clinical value of this technique.</p>
Comparative evaluation of band-based genotyping methods for Mycobacterium intracellulare and its application for epidemiological analysis
<p><em>Mycobacterium intracellulare</em> is a leading cause of nontuberculous mycobacterial pulmonary disease, with a rapidly increasing prevalence worldwide. This bacterium, commonly distributed in soil and water, is known to be transmitted through the environment rather than between people. Therefore, it is imperative to establish distinguishable genotyping methods to understand the clinical outcome, disease relapses, and epidemiology. Therefore, the present study comprised two steps. First, variable number tandem repetition (VNTR), VNTR-mycobacterial interspersed repetitive units (VNTR-MIRU), repetitive sequence based-PCR (rep-PCR) and pulsed field gel electrophoresis (PFGE) as band-based genotyping methods were performed using 19 <em>M. intracellualre</em> isolated from patients with PD. The comparative results of genotyping techniques and geographical characteristics in this study may provide fundamental information for the epidemiology of <em>M. intracellulare</em>.</p>
Data from: Is your phylogeny informative? Measuring the power of comparative methods
Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of these methods has become crucial to ensure that data quantity keeps pace with growing model complexity. Through simulations, we show that commonly applied model choice methods based on information criteria can have remarkably high error rates; this can be a problem because methods to estimate the uncertainty or power are not widely known or applied. Furthermore, the power of comparative methods can depend significantly on the structure of the data. We describe a Monte Carlo based method which addresses both of these challenges, and show how this approach both quantifies and substantially reduces errors relative to information criteria. The method also produces meaningful confidence intervals for model parameters. We illustrate how the power to distinguish different models, such as varying levels of selection, varies both with number of taxa and structure of the phylogeny. We provide an open-source implementation in the pmc ("Phylogenetic Monte Carlo") package for the R programming language. We hope such power analysis becomes a routine part of model comparison in comparative methods.
Obtained data from research comparing the effectiveness of extrinsic methods of motivation on video games
Open the record for dataset details and reuse information.
Comparative evaluation of species delimitation methods and phylogeny of the genus Agrilus (Coleoptera: Buprestidae) from China
<p><span>Table S1. Primer information. Table S2. PCR reaction conditions for COI.<span> Table S3. PCR reaction conditions for CYTB. </span>Table S4.<span> Information of <em>Agrilus</em> species collected from China. Figure S1. Comparison of results of four methods (ABGD, ASAP, jMOTU, bPTP) based on COI. Figure S2. Comparison of results of four methods (ABGD, ASAP, jMOTU, bPTP) based on CYTB. Figure S3. ML tree based on the concatenated sequences of three genes (COI, CYTB and 28S).</span> The DNA sequences of COI, CYTB and 28S used in this study are also provided.</span></p>
Dataset comparing different skewness methods tested in "Quantifying and comparing radiation damage in the Protein Data Bank"
<p>Dataset comparing five different skewness metrics (including the Bnet metric) across 23 radiation damage datasets in the publication "Quantifying and comparing radiation damage in the Protein Data Bank"</p>
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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.