.. Tadbit documentation master file, created by sphinx-quickstart on Tue Jan 15 18:23:49 2013. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive.

Welcome to TADbit's documentation!

TADbit is a computational package that deals with 3C-based data (more specifically Hi-C data). It handles all the steps from the alignment of paired-end reads to the detection of Topologically Associating Domain (TAD) borders, compartments and three-dimensional modeling of chromatin based on interaction matrices. The different steps:

  • preprocessing of paired-end reads from Hi-C experiment
  • alignment of the reads using GEM
  • fitering of the mapped reads
  • construction of interaction matrices and normalization
  • the identification of TAD borders and compartments
  • the 1D and 2D comparison of TADs
  • the three-dimensional modeling of the chromatin

The library has been designed to be used by researchers with minimal level of expertise in computer science. A set of the all-in-one scripts (called TADbit tools) allow to run a full analysis in one single command line.

On the other hand, advanced users may produce their own scripts using the TADbit API.

Documentation index:

.. epigraph:: .. toctree:: :maxdepth: 3 install tutorial tools reference/index biblio