defiant

Differential methylation: Easy, Fast, Identification and ANnoTation

by David E. Condon and Kyoung-Jae Won, University of Pennsylvania, 2015-2026. Email Dave at dec986@gmail.com with questions/complaints/suggestions. This has been published in BMC Bioinformatics: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2037-1

Defiant is designed to identify differentially methylated regions as quickly and as easily as possible. It was designed to make the process as easy as possible on the end user, and to enable DMR detection without having to use (and pay for) supercomputing resources.

installation

Download the repository and compile it with make on a Linux command line:

git clone https://github.com/hhg7/defiant && cd defiant && make

which will compile an executable “defiant” for your system. make check runs a quick test of the executable, and make install copies it to /usr/local/bin (make install PREFIX=$HOME/.local if you don’t have root). make OPENMP=1 compiles Defiant to run multiple options on multiple CPU (cf. -cpu), and make CC=clang compiles with clang instead of gcc. The Makefile lists other…