CEMBA Data Processing (0.1.2)

• Data mapping
• Data integration using xarray
• Data preprocessing, computation and visualization
• Regulatory region analysis

Giant workflow

• Stage 1 Mapping and QC. Prepare single cell base level methylation raw data.
• Stage 2 Single cell level analysis. Prepare dataset (xarray based) and preprocessing for clustering analysis.
• Stage 3 Cluster level analysis. Merge single cell data into cluster and identify the features of clusters.

Documentation

[TODO] Here

Get Start

Before install this package, please install Anaconda to get most of the required python packages. Python 3.6 or above is needed, old version won't work.

# install
git clone https://github.com/lhqing/cemba_data.git
cd cemba_data
python setup.py install

# to use the command line interface
yap -h

# to use cemba_data as a python module
import cemba_data as cd
from cemba_data.data.dataset import Dataset, Study

# read a dataset
dataset = Dataset(path_to_dataset)

# read a study 
study = Study.from_file(path_to_study)
# or from data
study = Study(data, rows_dict, cols_dict, uns_dict, study_name)

For more information, see the documentation.

Important Reference

Single cell:

• scanpy
• AnnData

Methylation and Epigenomics:

• Methylpy
• REPTILE