EACO (Enrichment Analysis for Customized Organism) package Manual

 

1. Introduction

EACO package is designed aimed to do enrichment analysis to fulfill the following features through three steps:

 

1. data preparation step:

1.1 filtering the redundancy of the gene sets

1.2 unify the input gene sets file format, which will enable this package can be used for any sequenced genomes

 

2. enrichment step

2.1 Integrate the latest algorithm, which is always developed initially for model organisms

 

3. visualization step

3.1 using bar or heatmap to visualize the comparisons integrating many samples.

 

In general, this package is written using Perl/R programming language, which will guarantee it can be run on all operating system.

2. Installation

The installation is simple un-compress it after you download it from here.

 

tar -zxf EACO_r20150101.tar.gz

3. Running examples

The examples are in the example directory. The following give out the explanation of this directory.

00.data the predefined test data

01.prep the preparation step

02.Enrich the enrichment step

03.Visualize the visualization step

4. Questions and suggestions

Any questions and suggestions are appreciated.

 

Pengcheng Yang

yangpc [AT] mail.biols.ac.cn