Bioinformatics tools for Python developed at the MPI for Biology of Ageing
Project description
## AGEpy [![Build Status](https://travis-ci.org/mpg-age-bioinformatics/AGEpy.svg?branch=master)](https://travis-ci.org/mpg-age-bioinformatics/AGEpy) [![PyPI version](https://badge.fury.io/py/AGEpy.svg)](https://badge.fury.io/py/AGEpy)
This python package contains Bioinformatics tools developed at the
Bioinformatics Core Facility of the Max Planck Institute for Biology of Ageing.
> Max Planck Institute for Biology of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
#### Read the Docs
We have started introducing some documentation [here]( https://github.com/mpg-age-bioinformatics/AGEpy/wiki).
#### Installation
###### pip
```bash
pip install https://github.com/mpg-age-bioinformatics/AGEpy/archive/0.6.0.tar.gz --user
```
###### github
Get the latest release from github:
```bash
git clone https://github.com/mpg-age-bioinformatics/AGEpy
```
Install:
```bash
cd AGEpy
python setup.py install --user
```
and then update to the latest release whenever required with:
```bash
cd AGEpy
git pull
python setup.py install --user --force
```
Alternatively you can also install the package with a symlink, so that changes
to the source files will be immediately available to users of the package on
your system:
```bash
cd AGEpy
python setup.py develop --user
```
Be aware that with the develop option you won't be able to properly update once new scripts are added.
#### Example usage
```python
import AGEpy as age
gtf=age.readGTF("/path/to/file.gtf")
gtf.head()
```
#### Help
In bash:
```bash
pydoc AGEpy.AGEpy
```
In python:
```python
help("AGEpy.AGEpy")
```
#### Scripts
* `david` a script to perform enrichment analysis from the DAVID database.
The usage is described in the script's help output called via `david --help`.
More information at: https://github.com/mpg-age-bioinformatics/AGEpy/wiki/david
* `bit` The [b]ermuda [i]nformation [t]riangle is a git-based tool for the management of code and data.
Check out https://github.com/mpg-age-bioinformatics/AGEpy/wiki/bit
This python package contains Bioinformatics tools developed at the
Bioinformatics Core Facility of the Max Planck Institute for Biology of Ageing.
> Max Planck Institute for Biology of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
#### Read the Docs
We have started introducing some documentation [here]( https://github.com/mpg-age-bioinformatics/AGEpy/wiki).
#### Installation
###### pip
```bash
pip install https://github.com/mpg-age-bioinformatics/AGEpy/archive/0.6.0.tar.gz --user
```
###### github
Get the latest release from github:
```bash
git clone https://github.com/mpg-age-bioinformatics/AGEpy
```
Install:
```bash
cd AGEpy
python setup.py install --user
```
and then update to the latest release whenever required with:
```bash
cd AGEpy
git pull
python setup.py install --user --force
```
Alternatively you can also install the package with a symlink, so that changes
to the source files will be immediately available to users of the package on
your system:
```bash
cd AGEpy
python setup.py develop --user
```
Be aware that with the develop option you won't be able to properly update once new scripts are added.
#### Example usage
```python
import AGEpy as age
gtf=age.readGTF("/path/to/file.gtf")
gtf.head()
```
#### Help
In bash:
```bash
pydoc AGEpy.AGEpy
```
In python:
```python
help("AGEpy.AGEpy")
```
#### Scripts
* `david` a script to perform enrichment analysis from the DAVID database.
The usage is described in the script's help output called via `david --help`.
More information at: https://github.com/mpg-age-bioinformatics/AGEpy/wiki/david
* `bit` The [b]ermuda [i]nformation [t]riangle is a git-based tool for the management of code and data.
Check out https://github.com/mpg-age-bioinformatics/AGEpy/wiki/bit
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