scdynomics.utils.data.reader

Methods to read in data.

author: jy

Functions

csv([path, sep, mode])	Extract GEX data from CSV files.
mex([path, scmultiomics])	Read in 10x MEX data.
mtx(file[, shape])	Read in a mtx file.
scMultiomics_10x_h5([path])	Read in 10x H5 data.
scMultiomics_10x_mex([path])	Read in 10x MEX data.
scMultiomics_csv_split(rna_path, atac_path)	Extract data from CSV files.
scMultiomics_mex_split([rna_path, atac_path])	Extract data from MEX (.tar.gz) files.
tsv(file[, header])	Read in a tsv file.

scdynomics.utils.data.reader.csv(path: str = None, sep: str = ',', mode: str = 'gex')

Extract GEX data from CSV files. scRNA and scATAC data are stored in separate files.

scdynomics.utils.data.reader.mex(path: str = None, scmultiomics: bool = True)

Read in 10x MEX data.

scdynomics.utils.data.reader.mtx(file, shape: set = None)

Read in a mtx file.

scdynomics.utils.data.reader.scMultiomics_10x_h5(path: str = None)

Read in 10x H5 data. Tested with 10x datasets, not sure what out other data.

scdynomics.utils.data.reader.scMultiomics_10x_mex(path: str = None)

Read in 10x MEX data. Tested with 10x datasets, not sure what out other data.

Extract data from MEX (.tar.gz) file.

scdynomics.utils.data.reader.scMultiomics_csv_split(rna_path: str, atac_path: str, sep: str = ',')

Extract data from CSV files. scRNA and scATAC data are stored in separate files.

scdynomics.utils.data.reader.scMultiomics_mex_split(rna_path: str = None, atac_path: str = None)

Extract data from MEX (.tar.gz) files. scRNA and scATAC data are stored in separate files.

NOT FINISHED!

scdynomics.utils.data.reader.tsv(file, header=None)

Read in a tsv file.