An information-theoretic tool for analyzing DNA methylation sequencing data.
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A julia port of the informME software package. The original informME is written in MATLAB, bash, C++, and R. By porting the code to julia, we hope to streamline the software, and remove the requirement that the user has a MATLAB software license.
⚠️ WARNING! THIS PACKAGE IS A WORK IN PROGRESS. FOR NOW, YOU SHOULD USE THE EXTENSIVELY TESTED MATLAB VERSION AVAILABLE HERE: https://github.com/GarrettJenkinson/informME
Samtools must be installed and on your system path.
The only unregistered julia dependency is QuadDIRECT which can be installed by typing ']' without quotes in the julia repl to bring up the pkg prompt and typing
pkg> add https://github.com/timholy/QuadDIRECT.jl.gitFor now, InformMe.jl is an unregistered package, and should be installed from the git repository at the pkg prompt:
pkg> add https://github.com/GarrettJenkinson/InformMe.jlor if you have a local clone of the repository:
pkg> add /path/to/local/repo/InformMe.jlthe installation can be tested at the pkg prompt by running
pkg> test InformMe- STABLE — documentation of the most recently tagged version.
- DEVEL — documentation of the in-development version.
All code except for the maxent algorithm (contained in /src/maxent.jl) is GPLv3 licensed. The maxent algorithm has the following licensing information in its header:
# Permission was provided by the author, Ali Mahammad-Djafari,
# to modify and distribute this code with the informME method's
# code. The original MATLAB code has been ported by Garrett Jenkinson
# to the julia language. Contact the original author
# directly for use outside of informME.
#
# Author's website:
# http://djafari.free.fr/index.htm
#
# Author's paper with source code:
# Mohammad-Djafari A. (1992) A Matlab Program to Calculate the Maximum Entropy Distributions. In: Smith C.R., Erickson G.J., Neudorfer P.O. (eds) Maximum Entropy and Bayesian Methods. Fundamental Theories of Physics (An International Book Series on The Fundamental Theories of Physics: Their Clarification, Development and Application), vol 50. Springer, Dordrecht
See CITATION.bib for the bibtex formatted citations. If using the package in an academic setting, please be sure to cite the relevant papers:
[1] Jenkinson, G., Pujadas, E., Goutsias, J., and Feinberg, A.P. (2017), Potential energy landscapes identify the information-theoretic nature of the epigenome, Nature Genetics, 49: 719-729.
[2] Jenkinson, G., Abante, J., Feinberg, A.P., and Goutsias, J. (2018), An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data, BMC Bioinformatics, 19:87, https://doi.org/10.1186/s12859-018-2086-5.
[3] Jenkinson, G., Abante, J., Koldobskiy, M., Feinberg, A.P., and Goutsias, J. (2019), Ranking genomic features using an information-theoretic measure of epigenetic discordance, BMC Bioinformatics, 20:175, https://doi.org/10.1186/s12859-019-2777-6.