Triple-Negative Breast Cancer
1535 cells from six fresh triple-negative breast cancer tumors.
openproblems_v1
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Description
1535 cells from six TNBC donors by (Wu et al., 2021). This dataset includes cytokine activities, inferred using a multivariate linear model with cytokine-focused signatures, as assumed true cell-cell communication (Dimitrov et al., 2022).
Preview
An AnnData object with n_obs × n_vars = 42512 × 28200 with slots:
obs: cell_type, size_factors
obsp: knn_connectivities, knn_distances
obsm: X_pca
varm: pca_loadings
layers: counts, normalized
| Name | Description | Type | Data type | Size |
|---|---|---|---|---|
| obs | ||||
cell_type | Classification of the cell type based on its characteristics and function within the tissue or organism. | vector | category | 42512 |
size_factors | The size factors created by the normalisation method, if any. | vector | float32 | 42512 |
| var | ||||
feature_name | A human-readable name for the feature, usually a gene symbol. | vector | object | 28200 |
hvg | Whether or not the feature is considered to be a 'highly variable gene' | vector | bool | 28200 |
hvg_score | A ranking of the features by hvg. | vector | float64 | 28200 |
| obsp | ||||
knn_connectivities | K nearest neighbors connectivities matrix. | sparsematrix | float32 | 42512 × 42512 |
knn_distances | K nearest neighbors distance matrix. | sparsematrix | float64 | 42512 × 42512 |
| obsm | ||||
X_pca | The resulting PCA embedding. | densematrix | float32 | 42512 × 50 |
| varm | ||||
pca_loadings | The PCA loadings matrix. | densematrix | float32 | 28200 × 50 |
| layers | ||||
counts | Raw counts | sparsematrix | float32 | 42512 × 28200 |
normalized | Normalised expression values | sparsematrix | float32 | 42512 × 28200 |
| 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 | |
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