<commit_before># Dots

Dots is a Python package for working with microarray data. 
Its back-end is a standalone package for reading in, normalisation, statistical 
analysis and plotting of Agilent single-colour microarray data. Its front-end
isn't finished yet (more on that below).

## Installation

Dots has a number of dependencies including NumPy and SciPy and the least painless
way of getting these is to use the 
[Anaconda Python distribution](https://store.continuum.io/cshop/anaconda/) which includes
NumPy and SciPy and a couple of the other required dependencies like Pandas, Scikit-learn
and Bokeh.

Once you've downloaded and installed Anaconda, you can install the Dots package as follows:

```
git clone https://github.com/sandyjmacdonald/dots_for_microarrays
cd dots_for_microarrays
sudo python setup.py install
```

Setuptools should take care of the dependencies but, in testing, I've found the NumPy, SciPy
and Scikit-learn installations to be problematic, hence my recommendation of using Anaconda
to relieve those headaches.

Once you have Anaconda, if you'd like to install and use Dots in a fenced-off virtual 
environment that won't interfere with anything else, then you can do so as follows:

```
conda create --yes -n dots_env python=2.7
source activate dots_env

git clone https://github.com/sandyjmacdonald/dots_for_microarrays
cd dots_for_microarrays
sudo python setup.py install
```

To test that the installation has worked, you can run Nosetests as follows:
<commit_msg>Least painful, not least painless. Thanks, Toby!<commit_after># Dots

Dots is a Python package for working with microarray data. 
Its back-end is a standalone package for reading in, normalisation, statistical 
analysis and plotting of Agilent single-colour microarray data. Its front-end
isn't finished yet (more on that below).

## Installation

Dots has a number of dependencies including NumPy and SciPy and the least painful
way of getting these is to use the 
[Anaconda Python distribution](https://store.continuum.io/cshop/anaconda/) which includes
NumPy and SciPy and a couple of the other required dependencies like Pandas, Scikit-learn
and Bokeh.

Once you've downloaded and installed Anaconda, you can install the Dots package as follows:

```
git clone https://github.com/sandyjmacdonald/dots_for_microarrays
cd dots_for_microarrays
sudo python setup.py install
```

Setuptools should take care of the dependencies but, in testing, I've found the NumPy, SciPy
and Scikit-learn installations to be problematic, hence my recommendation of using Anaconda
to relieve those headaches.

Once you have Anaconda, if you'd like to install and use Dots in a fenced-off virtual 
environment that won't interfere with anything else, then you can do so as follows:

```
conda create --yes -n dots_env python=2.7
source activate dots_env

git clone https://github.com/sandyjmacdonald/dots_for_microarrays
cd dots_for_microarrays
sudo python setup.py install
```

To test that the installation has worked, you can run Nosetests as follows:

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{'dir': 'git-commits-cleaned', 'id': '2287245', 'n_tokens_mistral': 905, 'n_tokens_neox': 828, 'n_words': 404}