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3 results for “Eukaryota”
SILVA_123 Eukaryota taxonomic training data formatted for DADA2; plus version with (uncurrated) additional sequences
<p>This is the Silva123 taxonomy reformatted to work with eukaryote sequences for dada2:</p> <p><a href="https://zenodo.org/api/files/4f873b5b-fe02-4344-8c8b-c723c3caba67/SILVA_123_dada2.fasta">SILVA_123_dada2.fasta </a></p> <p>It has been created using a script available <a href="https://github.com/derele/AA_Hyena/blob/master/R/convert_silva_taxonomy.r">here</a>.</p> <p>To increase coverage (Silva has a low coverage for eukaryotes). Uncurrated additional sequences similar to ASVs found in the intestine of hyenas (BLAST) have been added. The script used for taxonomic annotation of these sequences is available <a href="https://github.com/derele/AA_Hyena/blob/master/scripts/blast2alltax_outfmt11.pl">here</a>. The file containing these additional (uncurrated!) sequences is:</p> <p><a href="https://zenodo.org/api/files/4f873b5b-fe02-4344-8c8b-c723c3caba67/SILVA_123_dada2_exp.fasta?versionId=78a7526a-72e0-4707-ab5c-297671b5ff13">SILVA_123_dada2_exp.fasta </a></p> <p>This expanded file has been used for taxonomic annotation in: </p> <p><a href="https://doi.org/10.3389/fcimb.2017.00262">Heitlinger, E., Ferreira, S., Thierer, D., Hofer, H., & East, M. L. (2017). The intestinal eukaryotic and bacterial biome of spotted hyenas: the impact of social status and age on diversity and composition. <em>Frontiers in cellular and infection microbiology</em>, <em>7</em>, 262.</a></p>
Eukaryota, Luca, Vertebrata and Fungi Species Tree used in Quest for Orthologs Benchmarking
<p>Eukaryota, Luca, Vertebrata and Fungi Species Tree used in Quest for Orthologs Benchmarking by the 2018 event workflow (https://github.com/qfo/benchmark-webservice/tree/elixir). It is used specifically by the old variant of the generalized species tree discordance benchmark and defines the multifurcating reference species tree with collapsed edges for some of the more debated splits.</p>
Eukaryota, Luca, Vertebrata and Fungi Species Tree used in Quest for Orthologs Benchmarking
<pre>Eukaryota, Luca, Vertebrata and Fungi Species Tree used in Quest for Orthologs Benchmarking by the 2018 event workflow (https://github.com/qfo/benchmark-webservice/tree/elixir). It is used specifically by the old variant of the generalized species tree discordance benchmark and defines the multifurcating reference species tree with collapsed edges for some of the more debated splits.</pre>
ScienceDex guides
Understand access before you commit
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.