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16 results for “AnnData”
AnnData files for "Human dermal fibroblast subpopulations are conserved across single-cell RNA sequencing studies"
<p>AnnData files for "Human dermal fibroblast subpopulations are conserved across single-cell RNA sequencing studies". </p> <p>Includes Joined dataset with all four datasets at once.</p>
Converting NCBI Data to the AnnData Format
<p>Input dataset for the tutorial "Converting NCBI data to the AnnData Format" hosted on the Galaxy Training Network</p>
Brain Transcriptome Single-cell (BTS) Atlas: Anndata, Seurat Object, CellTypist model, and Disorder Risk Geneplot
<p>Brain Transcriptome Single-cell Atlas (BTS) Anndata, Seurat object, and Celltypist model for further use of the atlas. The Celltypist model can be utilized to accurately annotate cell types in new datasets based on the atlas. Plots illustrating the expression profile for 3,380 neurological disorder risk genes across the atlas are also uploaded. Further availability for the data can be requested by the corresponding author.<br><br>This dataset is published in Kim, S., Lee, J., Koh, I.G. <em>et al.</em> An integrative single-cell atlas for exploring the cellular and temporal specificity of genes related to neurological disorders during human brain development. <em>Exp Mol Med</em> <strong>56</strong>, 2271–2282 (2024). https://doi.org/10.1038/s12276-024-01328-6</p>
Source_AnnData_file.h5ad
<p>Test AnnData for workflow. Dataset extracted from a published original work from: </p> <p>Silvin A, Chapuis N, Dunsmore G, et al. Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19. Cell. 2020 Sep;182(6):1401-1418.e18. DOI: 10.1016/j.cell.2020.08.002. PMID: 32810439; PMCID: PMC7405878.</p> <h3></h3>
Xenium benchmarking- xenium formatted to AnnData 1 (mouse_brain)
<p>This repository contains Xenium datasets formated to AnnData format for benchmarking the characteristics and performance of Xenium (Marco Salas et al., 2024). Please visit https://github.com/Moldia/Xenium_benchmarking to obtain further information about the datasets. On summary, AnnData contains the expression of profiled cells with some metadata, including spatial position. In adata.obs['spots'] we also include the position of decoded reads as well as some additional metadata and quality. </p> <p> </p> <p>This repository is the part 1/4 of all repositories containing the datasets used in the study already formated to AnnData</p>
Anndata object of 10x Mouse Brain 5k data set for scDGD training
<p>This data from 10x (5k Adult Mouse Brain Nuclei Isolated with Chromium Nuclei Isolation Kit, Single Cell Gene Expression Dataset by Cell Ranger 7.0.0, 2022) is comprised of 7377 cells from the adult mouse brain with 32285 features. Cell type annotations were approximated using CellTpyist with the `Developing_Mouse_Brain` reference model and majority voting. This resulted in 7 distinct cell types.</p>
Downsampled AnnData input file - Galaxy Training Material
<p>Downsampled input dataset for the Single Cell Data Formats Conversion tutorial on Galaxy Training Network. </p>
AnnData object for case study tutorials
<p>This dataset works for the Filter, Plot & Explore tutorial: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html</p>
Xenium benchmarking- xenium formatted to AnnData 2 (human breast datasets)
<p>This repository contains Xenium datasets formated to AnnData format for benchmarking the characteristics and performance of Xenium (Marco Salas et al., 2024). Please visit https://github.com/Moldia/Xenium_benchmarking to obtain further information about the datasets. On summary, AnnData contains the expression of profiled cells with some metadata, including spatial position. In adata.obs['spots'] we also include the position of decoded reads as well as some additional metadata and quality. </p> <p> </p> <p>This repository is the part 2/4 of all repositories containing the datasets used in the study already formated to AnnData</p>
Xenium benchmarking- xenium formatted to AnnData 3 (miscellaneous)
<p>This repository contains Xenium datasets formated to AnnData format for benchmarking the characteristics and performance of Xenium (Marco Salas et al., 2024). Please visit https://github.com/Moldia/Xenium_benchmarking to obtain further information about the datasets. On summary, AnnData contains the expression of profiled cells with some metadata, including spatial position. In adata.obs['spots'] we also include the position of decoded reads as well as some additional metadata and quality. </p> <p> </p> <p>This repository is the part 3/4 of all repositories containing the datasets used in the study already formated to AnnData</p>
Test Anndata file for Decoupler Pathway Inference
<p>Test Anndata file, generated by Decoupler Pathway Inference script for Galaxy Wrapper </p>
Case study 3 AnnData object
<p>Dataset for the Filter, Plot & Explore tutorial.</p>
Filtered AnnData
<p>Filtered AnnData object for GTN tutorial "Inferring single cell trajectories with Scanpy" </p>
AnnData set for single cell analysis tutorial
Open the record for dataset details and reuse information.
Depression study - anndata
Open the record for dataset details and reuse information.
anndata_microglia_human_fetuses
<p>Pseudogenes were retained in both adata_merge_genenames.h5ad and adata_merge_genenames_leiden.h5ad. </p> <p>adata_merge_genenames.h5ad: Normalization and log transformation were performed, followed by retention of the top 3000 highly variable genes. Gene IDs were then mapped to gene names. </p> <p>adata_merge_genenames_leiden.h5ad: same as adata_merge_genenames.h5ad + leiden clusters (n_neighbors=10, n_pcs=20)</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.