sci-CAR Mouse Kidney

sci-CAR profiles of 11k mouse kidney cells

openproblems_v1_multimodal

Info

openproblems_v1_multimodal/scicar_mouse_kidney
Cao et al. (2018)
423 MiB
02-02-2024
11296 × 29013

Used in

No related benchmarks found.

Description

Single cell RNA-seq and ATAC-seq co-profiling of 11k mouse kidney cells.

Preview

dataset_mod1 is an AnnData object with n_obs × n_vars = 11296 × 29013 with slots:

dataset_mod2 is an AnnData object with n_obs × n_vars = 11296 × 249448 with slots:

Reference

Dataset mod1

Name Description Type Data type Size
obs
batch A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. vector category 11296
cell_type Classification of the cell type based on its characteristics and function within the tissue or organism. vector category 11296
size_factors The size factors created by the normalisation method, if any. vector float32 11296
var
feature_name A human-readable name for the feature, usually a gene symbol. vector object 29013
hvg Whether or not the feature is considered to be a ‘highly variable gene’ vector bool 29013
hvg_score A ranking of the features by hvg. vector float64 29013
obsm
X_svd The resulting SVD embedding. densematrix float32 11296 × 100
layers
counts Raw counts sparsematrix float32 11296 × 29013
normalized Normalised expression values sparsematrix float32 11296 × 29013
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
normalization_id Which normalization was used atomic str 1

Dataset mod2

Name Description Type Data type Size
obs
batch A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. vector category 11296
cell_type Classification of the cell type based on its characteristics and function within the tissue or organism. vector category 11296
size_factors The size factors created by the normalisation method, if any. vector float64 11296
var
feature_name A human-readable name for the feature, usually a gene symbol. vector object 249448
hvg Whether or not the feature is considered to be a ‘highly variable gene’ vector bool 249448
hvg_score A ranking of the features by hvg. vector float64 249448
obsm
X_svd The resulting SVD embedding. densematrix float64 11296 × 100
layers
counts Raw counts sparsematrix float64 11296 × 249448
normalized Normalised expression values sparsematrix float64 11296 × 249448
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
normalization_id Which normalization was used atomic str 1

References

Cao, Junyue, Darren A. Cusanovich, Vijay Ramani, Delasa Aghamirzaie, Hannah A. Pliner, Andrew J. Hill, Riza M. Daza, et al. 2018. “Joint Profiling of Chromatin Accessibility and Gene Expression in Thousands of Single Cells.” Science 361 (6409): 1380–85. https://doi.org/10.1126/science.aau0730.