EpiTensor: constructing 3-D
interactions from 1-D epigenomes
is a software package that can construct 3-D interactions from 1-D
to represent high-dimensional epigenomic data of various assays in
multiple cell types, and the utilizes tensor decomposition to break the
tensor into cell-type, assay, and genomic locus subspaces. The genomic
locus subspace captures epigenomic patterns across distal loci and
is associated with 3-D interactions among regulatory elements
1. Installation (64-bit LINUX
1) Unzip the downloaded Epitensor package using the following
tar –zxvf epitensor.tar.gz to
unzip the package.
The folder "release" should now be available.
2) Download MATLAB Compiler Runtime (MCR,
use the following commands to install MCR:
Alternatively, you can install MCR non-interactively using
the following commands:
./install -mode silent -agreeToLicense yes
<MCRROOT> is the root directory of MCR (e.g.
When the installation is done, add the following line to
your .bashrc file:
3) Install R enviroment (http://www.r-project.org/)
The LINUX command "R" should now start the R environment
4) Once R is installed, type "R" in LINUX console to enter the R
environment. Use "install.packages("R.matlab")" to install "R.matlab"
Try "library("R.matlab")", and it should work in R
5) Download spp package (http://compbio.med.harvard.edu/Supplements/ChIP-seq/).
Install Boost C++ if not already installed.
use "R CMD INSTALL spp_1.10.tar.gz" in linux
console to install spp package
Try "library("spp")" and it should work in R environment
6) Download wigToBigWig
Only wigToBigWig is needed.
Edit your ~/.bashrc file to include:
<KENT> is the installation directory (e.g.
The command wigToBigWig should now work from the
7) Download MACS2 software (https://github.com/taoliu/MACS/wiki/Install-macs2)
and follow the instructions to install it.
Try the "macs2" command in LINUX and macs2 usage
instruction should pop out.
8) Download BEDTools (v2.17) (https://github.com/taoliu/MACS/wiki/Install-macs2).
EDIT your ~/.bashrc file to include:
PATH=$PATH; <BEDTOOLS>, where
<BEDTOOLS> is the installation directory (e.g.
9) Use "sh recompile.sh" command to compile est_bkgd.lambda.cpp file.
Try the command "mergeBed -?" in LINUX and mergeBed usage
instruction should pop out. The "-nms" should be listed as one of the
parameters. Please note that BEDTools of version later than
2.20 will not work because the "-nms" parameter is not available.
2. Run Epitensor:
Try out "demo2.bash" to predict tss-tss, tss-enhancer,
enhancer-enhancer interactions in H1, TBL, MSC, NPC, and IMR90
After temination in ~90 minutes, the "tss_tss_interaction.bed",
"tss_enh_interaction.bed", and "enh_enh_interaction" will be available
in the "out" directory.
The software package was tested on a workstation with Intel Xeon CPU
and 12 GB memory.