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3c_tutorial

Step by step command-line tutorial to process Hi-C data

bacchus

Tools for analysis of BACterial Chromosome HiC data. (BACCHUS)

centroid

Identification of centromere from chromosomal contact maps Marie-Nelly, Marbouty et al., Bioinformatics, 2014

chromosight

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

chromosight_analyses_scripts

Codes used to perform analyses in the Chromosight publication

dade

e_coli_analysis

Relates to the article by Lioy, Cournac et al., Cell, 2018 (Functional partitioning of a bacterial chromosome through the interplay of nucleoid- associated proteins and the condensin MukBEF)

ectocarpus_scripts

Scripts and materials needed to reproduce results and figures in the instaGRAAL showcase paper

graal

(check out instaGRAAL for a faster, updated program!) This program is from Marie-Nelly et al., Nature Communications, 2014 (High-quality genome assembly using chromosomal contact data), also Marie-Nelly et al., 2013, PhD thesis (https://www.theses.fr/2013PA066714)

hic-box

GUI-based pipeline for Hi-C data processing and visualization

hic_reassembler

hicontacts

HiContacts: R interface to cool files and analysis of Hi-C contacts

hicstuff

Simple library/pipeline to generate and handle Hi-C data.

instagraal

Large genome reassembly based on Hi-C data, continuation of GRAAL

metator

Metagenomic binning based on Hi-C data

pareidolia

Multi-sample change detection in Hi-C patterns

serpentine

Local, normalization-free contact map binning

transcription_t7_analysis

In this repository, we present the code for the analysis of study of the transcription's impact on Escherichia coli chromosome.