.. METALoci documentation master file, created by sphinx-quickstart on Tue Jul 2 15:11:21 2024. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to METALoci's documentation! ==================================== *Spatially auto-correlated signals in 3D genomes.* ==================================== METALoci relies on spatial autocorrelation analysis, classically employed in geostatistics, to describe how the variation of a variable depends on space at a global and local scales (e.g., identifying contamination hotspots within a city). METALoci repurposes this type of analysis to quantify spatial genome hubs of similar epigenetic properties. Briefly, the overall flowchart of METALoci consists of four steps: * First, a genome-wide Hi-C normalized matrix is taken as input and the top interactions selected. * Second, the selected interactions are used to build a graph layout (equivalent to a physical map) using the ``Kamada-Kawai algorithm`` with nodes representing bins in the Hi-C matrix and the 2D distance between the nodes being inversely proportional to their normalized Hi-C interaction frequency. * Third, epigenetic/genomic signals, measured as coverage per genomic bin (e.g., ChIP-Seq signal for H3K27ac), are next mapped into the nodes of the graph layout. * The fourth and final step involves the use of a measure of autocorrelation (specifically, the Local Moran’s I or ``LMI``) to identify nodes and their neighborhoods with an enrichment of similar epigenetic/genomic signals. METALoci is compatible with ``.cool``, ``.mcool`` and ``.hic`` Hi-C formats; and with ``.bed`` signal files. The signal used in METALoci may be any numerical signal (as long as it is in a .bed file, with the location of such signal). METALoci is meant to be use in a command line interface (CLI). Several scripts are available to run METALoci in a step-by-step fashion. Refer to the :ref:`tutorial` for more information about how to use it. The ``METALoci Python API`` is also available for more advanced users. .. toctree:: :maxdepth: 1 :caption: Contents: install tutorial cli_usage METALoci Python API