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27
datasets available to search
ShareScore release 0.9.0
Dataset results
27 results for “taxonomic profiling”
In silico mock communities for evaluation of taxonomic profilers across eukaryotes in the human microbiome
<p><em>In silico </em>mock communities generated with CAMISIM for benchmarking the performance of taxonomic profilers across prokaryotic (50 communities), eukaryotic (30 communities), and viral communities (10 communities) of the human microbiome. Metagenomes were generated using CAMISIM (Fritz et al., 2019), which simulates 2.1 Gb of Illumina 2 ×150 bp paired end reads with the default HiSeq 2500 error profile and a mean insert size of 200 bp.</p> <p><strong>Eukaryotic communities<br></strong>30 eukaryotic <em>in silico</em> metagenomes comprising up to 200 randomly sampled genomes from a set of 113 eukaryotic species (See Supplementary Table 2 from the paper) corresponding to the eukaryotic species within both CHAMP and MetaPhlAn 4 (Blanco-Míguez et al., 2023) databasess.</p> <p><strong>Prokaryotic and viral communities</strong></p> <p>In silico data for prokaryotic and viral communities from the human microbiome can be found here: <a href="https://doi.org/10.5281/zenodo.10777404">doi: 10.5281/zenodo.10777404</a></p> <p><strong>References</strong></p> <p>Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., et al. (2023). Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. <em>Nature Biotechnology 2023 41:11</em> 41, 1633–1644. doi: 10.1038/s41587-023-01688-w</p> <p>Fritz, A., Hofmann, P., Majda, S., Dahms, E., Dröge, J., Fiedler, J., et al. (2019). CAMISIM: Simulating metagenomes and microbial communities. <em>Microbiome</em> 7, 1–12. doi: 10.1186/S40168-019-0633-6/FIGURES/5</p>
Example file for taxonomic profiling
<p>This example file comprises 10,000 quality-controlled (processed with <code>Porechop</code> and <code>nanoq</code>) prokaryotic reads (fungal and other reads removed with <code>minimap2</code>), randomly selected from the R10.3 mock sample of <a href="https://lomanlab.github.io/mockcommunity/r10.html" target="_blank" rel="noopener noreferrer">Loman Lab Mock Community Experiments</a>.</p>
Lemur Database for Taxonomic Profiling (bacteria, archaea, fungi)
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Data from: Construction of a species-level tree of life for the insects and utility in taxonomic profiling
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Gold standard taxonomic profile of the CAMI 2 Mouse Gut Toy data set, samples 0-63
<p><strong>DataURL: </strong> https://data.cami-challenge.org/participate</p>
Taxonomic profiles for simulation experiments
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example file for taxonomic profiling
<p>This example file comprises 10,000 quality-controlled (processed with <code>Porechop</code> and <code>nanoq</code>) prokaryotic reads (fungal and other reads removed with <code>minimap2</code>), randomly selected from the R10.3 mock sample of <a href="https://lomanlab.github.io/mockcommunity/r10.html" rel="nofollow">Loman Lab Mock Community Experiments</a>.</p>
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.