https://github.com/firefly-cpp/pygetoolbox
Gene expression toolbox in Python
https://github.com/firefly-cpp/pygetoolbox
Last synced: 2 days ago
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Gene expression toolbox in Python
- Host: GitHub
- URL: https://github.com/firefly-cpp/pygetoolbox
- Owner: firefly-cpp
- License: bsd-2-clause
- Created: 2018-12-30T11:39:56.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2022-04-05T12:57:43.000Z (over 3 years ago)
- Last Synced: 2025-01-29T18:03:13.523Z (11 months ago)
- Language: Python
- Size: 60.4 MB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
# PyGEtoolbox - Gene expression toolbox in Python
## Objective
## Installation
python setup.py install
## Features
- Downloading GEO DataSets from Gene Expression Omnibus (GEO) ([see example](examples/download_SOFT_format.py))
- Downloading RAW format from GEO ([see example](examples/download_RAW_data.py))
- Downloading CEL files from GEO ([see example](examples/download_CEL_files.py))
- Parsing SOFT format ([see example](examples/parse_SOFT_format.py))
- Affymetrix probe set ID to gene id and gene description conversion ([see example](examples/affy_probe_set_id_to_gene_id.py))
- Differentially Expressed genes analysis (TODO)
## CODE EXAMPLES:
```python
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")
```
```python
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.
## References
Datasets were downloaded from Gene Expression Omnibus available at the following website: [https://www.ncbi.nlm.nih.gov/geo/](https://www.ncbi.nlm.nih.gov/geo/)
## License
This package is distributed under the BSD 2-Clause "Simplified" License.
## Disclaimer
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!