1k Peripheral blood mononuclear cells

Name	Description	Type	Data type	Size
obs
`size_factors`	The size factors created by the normalisation method, if any.	vector	float32	1087
var
`feature_name`	A human-readable name for the feature, usually a gene symbol.	vector	object	15099
`hvg`	Whether or not the feature is considered to be a 'highly variable gene'	vector	bool	15099
`hvg_score`	A ranking of the features by hvg.	vector	float64	15099
obsp
`knn_connectivities`	K nearest neighbors connectivities matrix.	sparsematrix	float32	1087 × 1087
`knn_distances`	K nearest neighbors distance matrix.	sparsematrix	float64	1087 × 1087
obsm
`X_pca`	The resulting PCA embedding.	densematrix	float32	1087 × 50
varm
`pca_loadings`	The PCA loadings matrix.	densematrix	float64	15099 × 50
layers
`counts`	Raw counts	sparsematrix	float32	1087 × 15099
`normalized`	Normalised expression values	sparsematrix	float32	1087 × 15099
uns
`dataset_description`	Long description of the dataset.	atomic	str	1
`dataset_id`	A unique identifier for the dataset. This is different from the `obs.dataset_id` field, which is the identifier for the dataset from which the cell data is derived.	atomic	str	1
`dataset_name`	A human-readable name for the dataset.	atomic	str	1
`dataset_organism`	The organism of the sample in the dataset.	atomic	str	1
`dataset_reference`	Bibtex reference of the paper in which the dataset was published.	atomic	str	1
`dataset_summary`	Short description of the dataset.	atomic	str	1
`dataset_url`	Link to the original source of the dataset.	atomic	str	1
`knn`	Supplementary K nearest neighbors data.	dict		3
`normalization_id`	Which normalization was used	atomic	str	1
`pca_variance`	The PCA variance objects.	dict		2

Download & explore

The processed dataset lives on the OpenProblems public S3 bucket, which is world-readable. Download the file directly, or copy its S3 URI to fetch it with your tool of choice.

dataset.h5ad 45.29 MiB

Download

s3://openproblems-data/resources/datasets/openproblems_v1/tenx_1k_pbmc/log_cp10k/dataset.h5ad

Used in

Denoising

References

10x Genomics. (2018). 1k PBMCs from a Healthy Donor (v3 chemistry). link ↗