Software

Software

[ Pathway Analysis with Circos for Functional Metagenomics (PACFM) ]

PACFM is a software tool developed for the analysis of biological pathways in metagenomics projects. It provides the users with an improved way of visualizing pathway abundance data in addition to presenting a wide array of methods for filtering and normalization.

Download

PACFM is available from the links below as compressed directories for Mac OS X (10.11), Windows 10 and the souce code can be accessed from the github page.

1. pacfm-0.0.1.macosx-10.11-intel.tar.gz
2. pacfm-0.0.1.win-10-x64.zip
3. Source

Installation

Mac OSX:

1. Download the tarball from the link above.
2. Open a terminal window and type:
tar -xzvf pacfm-0.0.1.macosx-10.11.tar.gz

Mac OSX:

1. Download the zip file and extract the source files.

Source:

1. Install python 2.7
2. Install perl (>= 5.8)
3. Install the latest wxpython release compatible with your OS, from the following website: http://www.wxpython.org/download.php
4. (Required for Circos) Install the perl modules by typing the following in a terminal window
cpan X::Y::Z
The module name X::Y::Z is replaced by one of the following:
Config::General, Font::TTF::Font, Math::Bezier, Math::VecStat, Readonly, Text::Format, Statistics::Basic, Set::IntSpan, Regexp::Common, SVG
5. Clone into the pacfm project on github by typing

Running

The GUI

Mac OSX

1. From the terminal window change your directory into the path which you extracted the content of the tarball.
cd /path/to/pacfm
2. Run pacfm from the command line.
./pacfm

Source

The Commandline Interface

*nix

1. Type the following command in a terminal window.

Usage

Please see the user manual!

Reference

If you use PACFM in your research please cite the following paper:

— Sanli, K., Sinclair, L., Nilsson, R. H., Mardinoglu, A., and Eiler, A. (2016). PACFM: Pathway Analysis with Circos in Functional Metagenomics. Manuscript.