Siegel-Lab / libBioSmoother

On-the-fly processing and visualization of interactome data.

libSmoother - The C++ library behind Smoother

Smoother is an interactive analysis and visualization software for contact mapping data. This repository, libSmoother, contains the backend C++ library that powers Smoother. The library takes care of all the time-sensitive computations. It is written in C++17 and offers seamless integration with Python 3.

Quick Start

create & activate a new environment (optional)

conda create -y -n smoother python=3.9
conda activate smoother

Install libSmoother (and all requirements) using pip. LibSmoother runs under Windows, Linux, and MacOS.

pip install libbiosmoother

Download 2 example smoother indices.

wget https://syncandshare.lrz.de/getlink/fi4kLPLjRjMTbRnij7PtyB/t_brucei_hi_c.smoother_index.zip
#wget https://syncandshare.lrz.de/getlink/fiMo5Zsj8baXjXpzD8Whic/m_musculus_radicl_seq.smoother_index.zip

conda install unzip
unzip t_brucei_hi_c.smoother_index.zip
#unzip m_musculus_radicl_seq.smoother_index.zip

Export a picture from one of the indices

libbiosmoother export t_brucei_hi_c-c -f png
#libbiosmoother export m_musculus_radicl_seq -f png

Full Documentation

Since Smoother and libSmoother are designed as one package, they share documentation. Hence, for more information and in-depth instructions, check out Smoother's manual.

Cite

If you use Smoother in your research, please cite: @todo