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ShareScore release 0.9.0
Dataset results
4 results for “Cellxgene VIP”
Cellxgene VIP snRNA-seq demo dataset for visualization and DE analysis
<p>H5ad file can be used as demo input for Cellxgene VIP. Dataset was the re-process from Schirmer et al Nature 2019 paper by using the raw fastq files. In order to reproduce the h5ad file, details could be found in https://github.com/interactivereport/cellxgene_VIP/blob/master/notebook/MS_Nature_Rowitch_snRNAseq.ipynb <br> Two rds files are also included here which are the input files for sample differential expression (DE) analysis scripts (glmmTMB and Nebula)</p>
Mouse Brain snRNASeq Demo Dataset for Cellxgene VIP
<p>snRNASeq data generated at Biogen from 3 control mouse brains. Each brain picked 3 brain regions.</p> <p>Animal IDs 1, 4 and 7</p> <p>Brain region codes:<br> W: WhiteMatter<br> H: Hippo<br> G: GreyMatter</p> <p>10X standard mm10 (3.0.0) reference was used, on cellranger 5.0.0 with --include-introns on.<br> </p>
Mouse Brain Visium Demo Dataset for Cellxgene VIP
<p>Visium data generated from 3 control mouse full half brains</p> <p>Animal IDs 13, 14 and 53</p> <p>10X standard mm10 (2020-A) reference and spaceranger 1.1.0 was used<br> </p>
10X Genomics Human Visium Spatial Transcriptomics Demo Dataset for Cellxgene VIP
<p>4 Visium Spatial Transcriptomics datasets downloaded 10X Genomics data site ,and organized in the way to be used for Cellxgene VIP input.</p> <p>10X_demo_data_Breast_Cancer_Block_A_Section_1<br> 10X_demo_data_Breast_Cancer_Block_A_Section_2<br> 10X_demo_data_Human_Heart<br> 10X_demo_data_Human_Lymph_Node<br> </p>
ScienceDex guides
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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.