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.
Datasets were downloaded from Gene Expression Omnibus available at the following website: https://www.ncbi.nlm.nih.gov/geo/
This package is distributed under the BSD 2-Clause "Simplified" License.
This framework is provided as-is, and there are no guarantees that it fits your purposes or that it is bug-free. Use it at your own risk!