https://github.com/edawson/firehose

A collection of scripts for munging genomic and epigenetic data from the Broad Firehose.
https://github.com/edawson/firehose

Last synced: 4 days ago
JSON representation

A collection of scripts for munging genomic and epigenetic data from the Broad Firehose.

• Host: GitHub
• URL: https://github.com/edawson/firehose
• Owner: edawson
• License: gpl-2.0
• Created: 2014-07-31T17:35:52.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2014-09-07T03:56:40.000Z (about 10 years ago)
• Last Synced: 2023-04-04T14:14:09.982Z (over 1 year ago)
• Language: Python
• Size: 215 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
Firehose_Preprocessing

======================

A collection of scripts for munging genomic and epigenetic data from

the Broad Firehose.

## Description and Motivation

The Broad Institute of MIT and Harvard provides near-monthly releases of 

pre-processed data from The Cancer Genome Atlas. Firehose remains the 

most convenient way to programatically download data from TCGA, but often 

additional preprocessing is needed to make analysis using R or python

convenient. This package provides a set of scripts for processing, cleaning,

and transforming data from the Broad Firehose site to make it easier to perform

analyses.

## Dependencies

To run any scripts in this package you'll need to install a few dependencies. First,

make sure you're running a recent version of Python (preferably from the 2.7 generation.

Next, you'll need to install a few commonly-used Python libraries for data analysis:

1. NumPy

2. SciPy

3. PANDAS

4. Matplotlib

On Ubuntu, these may in turn have some other dependencies such as:

1. python-dev

2. build-essential

The easiest way to install all of these is with a combination of APT and pip:

**NB: Always be careful and responsible using sudo**

```sudo apt-get install python-dev build-essential python-pip```

```sudo pip install numpy```

```sudo pip install scipy```

```sudo pip install pandas```

```sudo pip install matplotlib```

## Installation

Now you're ready to install the Firehose package:

```git clone https://github.com/edawson/Firehose.git```

Right away you can run scripts out of the Firehose directory, but if you'd like

to link them into /usr/bin/ and run them anywhere you can do this:

```sudo ln -s "```

That's it! Currently there are no options for fine-tuning processing because these scripts try

to stay as minimalistic as possible. As time goes on usage may be subject to change, but

the above usage will **always** perform the standard transformations.  

Running the FirehosePreprocess script will perform the batch preprocessing of the entire set of files

(miRNA, mRNA, CNV, methylation, and MAF). Its usage is a little ugly but will be improved upon in the

future. You'll need to modify the variables directly at the top of the script; I promise to make this better

as time permits.

## Contacting the Author

If you use these scripts please make sure to credit where they came from:

>Eric T. Dawson  

>github.com/edawson/Firehose  

>erictdawson.com

If you would like to contact the author for comments, criticism, or praise, he can be reached

through his website above.

## Acknowledgements

These scripts were developed during the author's stint as a student intern at The Ontario

Institute for Cancer Research. They are a (nearly) direct port of scripts originally produced

by Dr. Guanming Wu.