monprin/camoco repository overview

⁠Camoco

⁠Co-Analysis of Molecular Components

Camoco is a python library for building and analyzing co-expression networks. Currently, networks are generally built from gene expression data, but given that the input to Camoco is simply a gene-by-sample expression matrix, there is not reason that the analysis couldn't include things like protein abundance or metabolites. Hence the name: co-analysis of molecular components. Very breifly, Camoco creates co-expression networks using table formatted expression data and and a few common genome data files:

Required Files:

• FPKM (or equivalent) CSV/TSV file
• GFF File

Optional Files:

• Gene Ontology (.obo and gene mapping)

Once co-expression networks are built, you can interact with the data using the included command line:

# If you are using the conda virtual environment
source activate camoco
# Run the command line interface to get an idea of how Camoco works
camoco --help

See more examples below in the CLI section.

Camoco is built almost entirely in Python and was designed to be modular and object based. This means that Camoco can also be used interactively from the shell using an interactive python session such as iPython. Just import the package!

import camoco as co
help(co.COB)

Object classes are well documented for inputs and outputs.

⁠Installation

⁠Docker

The easiest way to install Camoco is to use the included DockerFile. Download and install Docker⁠ on Linux, windows or Mac OS X. Using docker will ensure that Camoco is run in an environment closest to what it was developed in. After you have installed and tested docker, you should be able to build and run camoco:

# Download the repo
git clone https://github.com/schae234/Camoco.git
# Build the docker file (grab some coffee)
cd Camoco
docker build -t camoco .
# Run the docker image interactively
docker run -it camoco
# Inside docker image
souce activate camoco
camoco --help
source deactivate
# Exit the docker image
exit

⁠Virtual Environment

Alternatively, you can install Camoco using the included installation script. This script creates an anaconda based virtual environment which takes care of all required python packages as well as several of the external binaries and programs used by Camoco. Installation should be as easy as:

# Download and run install script
git clone https://github.com/schae234/Camoco.git
cd Camoco
# Follow instructions on screen
./install.sh
# Activate the virtual environment
source activate camoco
# Use CLI or run script
camoco --help
# deactivate virtual environment
source deactivate

You will need to add a few lines to your .bashrc in order for the conda environment to be available from your shell.

e.g.:

# Assuming your installed camoco to ~/.camoco
export LD_LIBRARY_PATH=~/.camoco/lib/:$LD_LIBRARY_PATH
export PATH=$BASE/bin:~/.camoco/conda/bin/:$PATH

The installation script accepts simple arguments: -b (default: ~/.camoco): the base directory to install camoco including storage for databases

Tagged releases are available on PyPi: pip install camoco.

⁠CLI

Once installed, the camoco command will be available through the terminal. See camoco --help for options!

⁠Tests

Unit tests within Camoco are implemented using the pytest framework. Unit tests as well as Build tests can be found in the test directory.

Tests can be run by executing py.test in the tests dir:

source activate camoco
cd tests
py.test

⁠Documentation

We acknowledge a lack of formal manual. We are writing this. However, the function definitions themselves are well commented throughout the code base. Questions and concerns about usage issued through github will be addressed! Contact us!

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