Gene expression toolbox in Python
PyGEtoolbox - Gene expression toolbox in Python
python setup.py install
- Downloading GEO DataSets from Gene Expression Omnibus (GEO) (see example)
- Downloading RAW format from GEO (see example)
- Downloading CEL files from GEO (see example)
- Parsing SOFT format (see example)
- Affymetrix probe set ID to gene id and gene description conversion (see example)
- Differentially Expressed genes analysis (TODO)
from PyGEtoolbox import * #downloading GSE from GEO series = Download() series.download_SOFT_format("GSE105008") #downloading GDS from GEO datasets = Download() datasets.download_SOFT_format("GDS2003") #downloading CEL file cel = Download() cel.download_CEL_file("GSM270781") #downloading RAW data raw_data = Download() raw_data.download_RAW_data("GSE41657")
from PyGEtoolbox import * a = Process_SOFT_format("../SOFT_format/GSE10714_family.soft.gz") # path to the data a.extract_metadata() a.print_data() a.extract_all_samples()
This project will be regularly updated during the 2019. Testing this package is more than welcome. Please report all bugs, suggestions and features that could be added.
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