scRNAseq#
scRNA-seq data analysis calculating gene expression, genetic noise
- class scRNAseq.CountsAnalysis(counts_file_path, genes=None)#
Analyse scRNA-seq counts data
- get_counts()#
Returns the counts
Returns#
- counts: pd.DataFrame
The single cell counts for genes (rows) and cells (columns)
- get_expression(cell_populations, genes=None)#
Returns the calculated gene expression
Parameters#
- cell_populations: dict
The cell populations with the lists or arrays of cells as values and arbitrary cell population keys as keys
- genes: list(str)
The list of genes to be used as indices of the counts, if None then all genes are used
Returns#
- x_mean: pd.DataFrame
The mean gene expression for genes (rows) and cell populations (columns)
- x_std: pd.DataFrame
The standard deviation of gene expression for genes (rows) and cell populations (columns)
- x_n: pd.DataFrame
The number of cells in the cell population for genes (rows) and cell populations (columns)
- x_cell_populations: dict
The used cell populations, which may differ from cell_populations if some cell keys are not found in the counts columns
- get_expression_noise(cell_populations, genes=None)#
Returns the calculated gene expression and genetic noise
Parameters#
- cell_populations: dict
The cell populations with the lists or arrays of cells as values and arbitrary cell population keys as keys
- genes: list(str)
The list of genes to be used as indices of the counts, if None then all genes are used
Returns#
- x_mean: pd.DataFrame
The mean gene expression for genes (rows) and cell populations (columns)
- x_std: pd.DataFrame
The standard deviation of gene expression for genes (rows) and cell populations (columns)
- x_n: pd.DataFrame
The number of cells in the cell population for genes (rows) and cell populations (columns)
- x_cell_populations: dict
The used cell populations, which may differ from cell_populations if some cell keys are not found in the counts columns
- noise: pd.DataFrame
The genetic noise for genes (rows) and cell populations (columns)
- noise_std: pd.DataFrame
The estimated error on genetic noise for genes (rows) and cell populations (columns)
- get_genes()#
Returns the genes
Returns#
- genes: pd.Series
The genes in the counts with names as values and Ensembl gene IDs as keys (index)
- get_noise(cell_populations, genes=None)#
Returns the calculated genetic noise
Parameters#
- cell_populations: dict
The cell populations with the lists or arrays of cells as values and arbitrary cell population keys as keys
- genes: list(str)
The list of genes to be used as indices of the counts, if None then all genes are used
Returns#
- noise: pd.DataFrame
The genetic noise for genes (rows) and cell populations (columns)
- noise_std: pd.DataFrame
The estimated error on genetic noise for genes (rows) and cell populations (columns)
- x_n: pd.DataFrame
The number of cells in the cell population for genes (rows) and cell populations (columns)
- x_cell_populations: dict
The used cell populations, which may differ from cell_populations if some cell keys are not found in the counts columns
- scRNAseq.get_expression_noise(counts, cell_populations, genes=None, do_noise=True)#
Returns the calculated gene expression and genetic noise
Parameters#
- counts: pd.DataFrame
The single cell counts for genes (rows) and cells (columns)
- cell_populations: dict
The cell populations with the lists or arrays of cells as values and arbitrary cell population keys as keys
- genes: list(str)
The list of genes to be used as indices of the counts, if None then all genes are used
- do_noise: bool
If the genetic noise and its estimated error shall be calculated and returned
Returns#
- x_mean: pd.DataFrame
The mean gene expression for genes (rows) and cell populations (columns)
- x_std: pd.DataFrame
The standard deviation of gene expression for genes (rows) and cell populations (columns)
- x_n: pd.DataFrame
The number of cells in the cell population for genes (rows) and cell populations (columns)
- x_cell_populations: dict
The used cell populations, which may differ from cell_populations if some cell keys are not found in the counts columns
- noise: pd.DataFrame
The genetic noise for genes (rows) and cell populations (columns)
- noise_std: pd.DataFrame
The estimated error on genetic noise for genes (rows) and cell populations (columns)