Hi there! I'm J. Sebastian Contreras, bioinformatic engineer and doctor in biotechnology.

Currently, I'm doing my postdoc at the Plant Genome Regulation Lab (Centro de Biotecnología Vegetal, UNAB)

I love programming and data science and apply these tools to biological sciences. My research focuses on deciphering the relationship between epigenetics and how they shape the promoter accessibility under plant stresses

Here you can find a list of software that I have developed (totally or partially.) It could be published or not.

• FRiP: Compute Fraction of Reads in Peaks (FRiP) for a ChIP/ATAC seq experiment given the alignment and peak file.

• Network AUPR: compute the Area Under a Precision-Recall curve based on a reference and a GENIE3 inferred network.

• Filtering GENIE3 results: Python script to filter the best x-percent of TFs directing the expression of a gene in a GENIE3 gene regulatory network.

• binarizeDF: A simple Python function to binarize a pandas data frame.

• RIP-MD: a VMD plugin to perform Residue Interaction Network for Molecular Dynamics trajectories. This was programmed under python2 and maybe it will not work in your system. The RIP-MD core for python3 can be found here

• Human and Mouse netwoks: Reference gene regulatory networks for these organisms made by the combination of the RegNetwork, TRRUST, and DoRothEA repositories

• Fly T-WEoN: A Cytoscape app that incorporates a filtering method to determine context-specific gene regulatory networks using Drosophila melanogaster epigenomic information

• Bacterial and archaeal regulatory networks: A web interface to visualize and download gene regulatory networks for bacteria and archaea