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.
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
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.
If you use Smoother in your research, please cite:
Markus R Schmidt, Anna Barcons-Simon, Claudia Rabuffo, T Nicolai Siegel, Smoother: on-the-fly processing of interactome data using prefix sums, Nucleic Acids Research, Volume 52, Issue 5, 21 March 2024, Page e23, https://doi.org/10.1093/nar/gkae008