Pinned Repositories
3C_tutorial
Step by step command-line tutorial to process Hi-C data
chromosight
Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
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)
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
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
Romain Koszul Laboratory's Repositories
koszullab/chromosight
Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
koszullab/instaGRAAL
Large genome reassembly based on Hi-C data, continuation of GRAAL
koszullab/hicstuff
Simple library/pipeline to generate and handle Hi-C data.
koszullab/metaTOR
Metagenomic binning based on Hi-C data
koszullab/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)
koszullab/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)
koszullab/pareidolia
Multi-sample change detection in Hi-C patterns
koszullab/HiC-Box
GUI-based pipeline for Hi-C data processing and visualization
koszullab/serpentine
Local, normalization-free contact map binning
koszullab/3C_tutorial
Step by step command-line tutorial to process Hi-C data
koszullab/chromosight_analyses_scripts
Codes used to perform analyses in the Chromosight publication
koszullab/ectocarpus_scripts
Scripts and materials needed to reproduce results and figures in the instaGRAAL showcase paper
koszullab/centroID
Identification of centromere from chromosomal contact maps Marie-Nelly, Marbouty et al., Bioinformatics, 2014
koszullab/HiContacts
HiContacts: R interface to cool files and analysis of Hi-C contacts
koszullab/bacchus
Tools for analysis of BACterial Chromosome HiC data. (BACCHUS)
koszullab/DADE
koszullab/HiC_reassembler
koszullab/transcription_T7_analysis
In this repository, we present the code for the analysis of study of the transcription's impact on Escherichia coli chromosome.