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3
datasets available to search
ShareScore release 0.7.1
Dataset results
3 results for “scanpy”
Stereo-seq E12.5_E1S3 bin 200 expression matrix (dgC Matrix), spatial locations (.csv), and h5ad file (scanpy flavor)
<p>Expression matrix in rds file format and spatial locations of E12.5_E1S3 downloaded from the Mouse Organogenesis Spatiotemporal Transcriptomic Atlas. Files were processed using an adapted version of the STOMICS Analysis Workflow (SAW) pipeline. </p>
Scanpy Parameter Iterator - Galaxy Training Material
<p>Input dataset for the Scanpy Parameter Iterator tutorial on Galaxy Training Network. It is an extension of <a href="https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html">Filter, Plot and Explore Single-cell RNA-seq Data</a> tutorial.</p>
Training data for "Clustering 3K PBMCs with Scanpy"
<p>Single-cell RNA-seq analysis is a rapidly evolving field at the forefront of transcriptomic research, used in high-throughput developmental studies and rare transcript studies to examine cell heterogeneity within a populations of cells. The cellular resolution and genome wide scope make it possible to draw new conclusions that are not otherwise possible with bulk RNA-seq.</p> <p>In this tutorial, we will investigate clustering of single-cell data from 10x Genomics, including preprocessing, clustering and the identification of cell types via known marker genes, using <a href="https://scanpy.readthedocs.io/en/stable/index.html">Scanpy</a> (<a href="http://0.0.0.0:4000/training-material/topics/transcriptomics/tutorials/scrna-scanpy-pbmc3k/tutorial.html#wolf2018scanpy">Wolf <em>et al.</em> 2018</a>). It is illustrated using a dataset of Peripheral Blood Mononuclear Cells (PBMC), extracted from a heal, freely available from 10X Genomics. The dataset contains 2,700 single cells sequencd using Illumina NextSeq 500. The raw sequences have been processed by <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger"><strong>cellranger</strong></a> pipeline from 10X to extract an unique molecular identified (UMI) count matrix.</p> <p> </p>
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.