Automated Stripe Identification from contact matrix.
Project description
StripeCaller
A Python implementation of the architectural stripe detecting algorithm described by Vian L et al [1].
Currently, this package contains 3 scripts: call-stripes, pileup-stripes and stripe-plot:
call-stripes
Call stripes from contact matrix. The only required input is the cool URI at certain resolution. The algorithm will detect horizontal (3’) and vertical (5’) stripes separately by searching for consecutive pixels with contact signals significantly higher than the local backgrounds. The output is a single file in bedpe format.
pileup-stripes
This script performs a pileup analysis on stripes.
stripe-plot
Visualize stripes on heatmap.
Installation
stripecaller is developed and tested on UNIX-like operating system, and following packages or softwares are required, which can be installed through conda <Miniconda installer
Python 3.5+
Multiprocess
Numpy
Scipy
Matplotlib
Cooler
First, add some additional channels:
$ conda config --add channels defaults $ conda config --add channels bioconda $ conda config --add channels conda-forge
Then execute the following command:
$ conda install multiprocess numpy scipy matplotlib cooler
Finally, install the stripecaller by pip:
$ pip install stripecaller
Usage
Open a terminal, type stripecaller -h for help information.
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