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ShareScore release 0.9.0
Dataset results
2 results for “Taxonomy Training”
RDP Classifier 2.14 and the RDP bacterial and archaeal taxonomy training set No. 19
<p>RDP Classifier 2.14 (August 2023) Release Note:</p><p>The Bacteria and Archaea hierarchy model used by RDP Classifier has been updated to training set No. 19. The new version has over 600 genera and 2500 species added since last version No. 18 released in July 2020. The information that is used to update the RDP taxonomy to training set version No. 19, and RDP Classifier version 2.14 came from publicly available scientific articles and public sequence repository, mostly from International Journal of Systematic and Evolutionary Microbiology (IJSEM), the All-Species Living Tree Project (LTP) and GenBank. </p><p>It is worth noting that most of the phyla have new names, according to article "</p><p>Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol. 2021 Oct;71(10). doi: 10.1099/ijsem.0.005056. PMID: 34694987."</p><p>In addition to the files to train and run the RDP Classifier, new file formats are made available to accommodate the needs of users:</p><p>1. A new file trainset19_072023_speciesrank.fa has been added to the release in RDPClassifier_16S_trainsetNo19_rawtrainingdata.zip. This file is NOT needed to train the classifier. In addition to sequences, it contains genus, species, strain, type status and taxonomy rank, which are useful for closest species identification using third-party tools (e.g. BLAST).</p><p>2. Two new files in RDPClassifier_16S_trainsetNo19_QiimeFormat.zip to retrain the RDP Classifier included in Qiime2 package.</p>
Lund Bladder Cancer Group - Lund Taxonomy 2023 Classifier - Training Data
<p>Raw and processed training data used for the Lund Taxonomy 2023 gene expression classifier for urothelial carcinoma.</p><p>The dataset contains the raw .CEL files for 3 Affymetrix Gene 1.0 ST cohorts: Lund2017 (n=307, GSE83586), Lund2020 (n=173, GSE128959), Lund2022 (n=310, 117 from GSE169455, 37 from GSE222073, and 156 previously unpublished samples). Code examples for RMA and SCAN.UPC normalization for Affymetrix Gene, Exon, and HTA2 arrays used in the study is included. Hybridization batch information is available for each array cohort.</p><p>The dataset contains Kallisto and Salmon transcript quantification files for 265 RNA-sequenced tumors and the tx2gene file+code for transcript to gene summarization using txImport</p><p> </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.