# CCBCGE
The goal of this python package is to provide quick, easy access to breast cancer gene expression data from OSF for analysis.
You can view this python package on its [PyPI Site](https://pypi.org/project/ccbcge/)
## Installation
Since this is a python package, you must have python installed on your computer. This package calls for Python 3.8 or greater.
To install this package, run the following command in your terminal:
```
pip install ccbcge
```
## Usage
There are four major functions that you can call.
1. `ChooseData()`
- This allows you see the list of data sets you can access and choose one to download.
- It returns two data sets: the gene expression data, then the meta data for that data set.
4. `ShowDataSets()`
- This shows the list of data sets you can access.
5. `importData(dataSet)`
- This takes as input the name of the data set you want to access.
- It returns the gene expression data of that name as a `pandas` data frame.
6. `importMeta(dataSet)`
- This takes as input the name of the data set you want to access.
- It returns the meta data for that data set as a `pandas` data frame.
The idea behind these functions is that you can access the data frame easily by name if you
already know which data set you want to access.
For those who do not know which data sets they want to access, however, they have the option
of seeing the data sets and choosing from them the one they want to work with.
If you want to use all of the data, you could write a simple for loop as follows:
```
for dataSet in dataSets:
geneData = importData(dataSet)
metaData = importMeta(dataSet)
# analyze the data here
```
## Dependencies
This package requires use of the following packages:
- `request`
- `pandas`
If you do not have them installed already, they will be installed for you.
## Development
Help for how to update this package is found in a [Developers File](dev.md)
## License
This project is licensed under the Apache 2.0 License - see the [LICENSE](LICENSE) file for more information.
## Acknowledgements
The idea for this project came from a similar package from the Payne Lab at Brigham Young University, called `cptac`.
To find out more about that package, visit the [CPTAC Github repository](https://github.com/PayneLab/cptac/)
or the [CPTAC PyPI package](https://pypi.org/project/cptac/).
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"description": "# CCBCGE\r\n\r\nThe goal of this python package is to provide quick, easy access to breast cancer gene expression data from OSF for analysis.\r\n\r\nYou can view this python package on its [PyPI Site](https://pypi.org/project/ccbcge/)\r\n\r\n## Installation\r\n\r\nSince this is a python package, you must have python installed on your computer. This package calls for Python 3.8 or greater.\r\n\r\nTo install this package, run the following command in your terminal:\r\n```\r\npip install ccbcge\r\n```\r\n\r\n## Usage\r\n\r\nThere are four major functions that you can call.\r\n1. `ChooseData()`\r\n - This allows you see the list of data sets you can access and choose one to download.\r\n - It returns two data sets: the gene expression data, then the meta data for that data set.\r\n4. `ShowDataSets()`\r\n - This shows the list of data sets you can access.\r\n5. `importData(dataSet)`\r\n - This takes as input the name of the data set you want to access.\r\n - It returns the gene expression data of that name as a `pandas` data frame.\r\n6. `importMeta(dataSet)`\r\n - This takes as input the name of the data set you want to access.\r\n - It returns the meta data for that data set as a `pandas` data frame.\r\n\r\nThe idea behind these functions is that you can access the data frame easily by name if you \r\nalready know which data set you want to access.\r\n\r\nFor those who do not know which data sets they want to access, however, they have the option\r\nof seeing the data sets and choosing from them the one they want to work with.\r\n\r\nIf you want to use all of the data, you could write a simple for loop as follows:\r\n```\r\nfor dataSet in dataSets:\r\n geneData = importData(dataSet)\r\n metaData = importMeta(dataSet)\r\n\r\n # analyze the data here\r\n```\r\n\r\n\r\n## Dependencies\r\n\r\nThis package requires use of the following packages:\r\n- `request`\r\n- `pandas`\r\n\r\nIf you do not have them installed already, they will be installed for you.\r\n\r\n## Development\r\n\r\nHelp for how to update this package is found in a [Developers File](dev.md)\r\n\r\n## License\r\n\r\nThis project is licensed under the Apache 2.0 License - see the [LICENSE](LICENSE) file for more information.\r\n\r\n## Acknowledgements\r\n\r\nThe idea for this project came from a similar package from the Payne Lab at Brigham Young University, called `cptac`.\r\nTo find out more about that package, visit the [CPTAC Github repository](https://github.com/PayneLab/cptac/)\r\nor the [CPTAC PyPI package](https://pypi.org/project/cptac/).\r\n",
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