PyGEtoolbox - Gene expression toolbox in Python

Objective

Installation

python setup.py install

Features

• 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)

CODE EXAMPLES:

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()

Bugs

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.