pypairs.datasets.leng15

pypairs.datasets.leng15(mode='all', gene_sub=None, sample_sub=None)

Single cell RNA-seq data of human hESCs to evaluate Oscope [Leng15]

Total 213 H1 single cells and 247 H1-Fucci single cells were sequenced. The 213 H1 cells were used to evaluate Oscope in identifying oscillatory genes. The H1-Fucci cells were used to confirm the cell cycle gene cluster identified by Oscope in the H1 hESCs. Normalized expected counts are provided in GSE64016_H1andFUCCI_normalized_EC.csv.gz

Parameters:
mode : Optional[str]

sample selection mode:
  • ’all’ for all samples, default
  • ’sorted’ for all samples with known cell cycle (G2, S or G1)
  • ’unsorted’ for all samples with unknown cell cycle (H1)

gene_sub : Optional[Iterable[int]]

Index based array of subsetted genes

sample_sub : Optional[Iterable[int]]

Index based array of subsetted samples
Return type:

AnnData
Returns:

adata (AnnData) – Annotated data matrix containing the normalized gene counts