Dekker Lab's repositories
cworld-dekker
perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
matrix_paper
Scripts and notebooks used in Akgol Oksuz et al. paper
cLIMS-docker
cLIMS repository running on Docker Contaienrs
Zagelbaum_etal_NSMB_2022
Notebooks for Hi-C analyses related to "Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization".
Abramo_2019
some scripts and notebooks for the Abramo et al 2019 paper
Docker-Machines
Docker Files and docker-compose files for various machines
matrix_shared
collection of scripts, config files and other materials related to the Matrix project
MC-3C_scripts
Scripts used to process and analyse the data in the MC-3C paper
pita_project
hi-c related analysis for the PITA-project
Topo-II-Inhibition-Manuscript
Github Repo for Hi-C and MC-3C analysis scripts for the Topo II Inhibition Manuscript
chimera-tie-public
a split-read alignment process for mapping multi-chimeric reads
Single_cell_scripts
Xiangru's scripts and notebooks for single-cell
psb-sysbio-course-hic-part
Systems Biology Course matlab session
5C-CBFb-SMMHC-Inhib
Software tools, for 5C analysis, and 5C primers used in the paper CBFb-SMMHC-Inhib ...
allelic-rt-supplement
supplementary analysis for the allelic RT study
chimera-tie
a split-read alignment process for mapping multi-chimeric reads
CTCF_in_mitosis_GR_2018
Scripts
distiller-nf
a modular Hi-C mapping pipeline
DNATriangulation
A set of scripts for genome assembly
experimental
some experimental notebooks
higlass-manage
A utility script to manage local docker instances of HiGlass
negspy
Python NGS Repository
pairsamtools
CLI tools to process mapped Hi-C data