chromatin
There are 47 repositories under chromatin topic.
mdozmorov/HiC_tools
A collection of tools for Hi-C data analysis
open2c/cooler
A cool place to store your Hi-C
mdozmorov/HiC_data
A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
3DGenomes/TADbit
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
fl-yu/CUT-RUNTools-2.0
CUT&RUN and CUT&Tag data processing and analysis
tobiasrausch/ATACseq
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
tanjimin/C.Origami
C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
ay-lab/dcHiC
dcHiC: Differential compartment analysis for Hi-C datasets
open2c/polychrom
Chromosome polymer simulations and in silico capture experiments
meuleman/epilogos
Methods for summarizing and visualizing multi-biosample functional genomic annotations
XiaoTaoWang/HiCPeaks
A Python implementation for BH-FDR and HiCCUPS
XiaoTaoWang/TADLib
A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
3DGenomes/TADkit
3D Genome Browser
vaquerizaslab/chess
Comparison of Hi-C Experiments using Structural Similarity.
aertslab/PUMATAC
Pipeline for Universal Mapping of ATAC-seq
BogdanBintu/ChromatinImaging
Super-resolution chromatin tracing 2018
tzeitim/genome-blender
Scripts to create cartoons of 3D genomes
GryderArt/AQuA-HiChIP
Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.
pombo-lab/gamtools
Processing, quality control and analysis of GAM datsets
HuntsmanCancerInstitute/MultiRepMacsChIPSeq
Multiple-replica multiple-condition Macs2 ChIPSeq wrapper
raevskymichail/epi-impute
Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data
SansamLab-Pipelines-Genomics/Cut_And_Run_Analysis_SnakeMake
Step-by-step instructions and Snakemake pipeline for processing Cut&Run data
gtca/chame
Chromatin analysis module
Pasquali-lab/UMI4Cats
An R package for analyzing UMI-4C chromatin contact data.
aleskunder/topology_loop_caller
Chromatin loop caller using Topological Data Analysis based on Hi-C data
polly-code/DPDchrom
Reconstruction of 3D conformation of chromatin fiber using single cell Hi-C data
younglab/fourfold
4C-seq data processing and visualization pipeline
mireia-bioinfo/phdthesis_code
🖥️📚 WorkflowR site containing code and analyses produced throghout my PhD thesis.
YoussefAyachii/HiCDataAnalysis
Using chromatin-chromatin interaction scores generated by the Capture Hi-C technology, I developed this R code during my six week internship in the Spicuglia lab, part of the INSERM institute (TAGC) related to the Aix-Marseille University, France, in order to identify the DNA interactions happening between different regions, specifically the interaction of the OAS3 Epromoter with its target promoters OAS1 and OAS2, before and after IFN alpha stress stimulation and then to figure out the changes of the 3D chromatin organization upon this stress stimulation.
bhardwaj-lab/scChICflow
Workflow for processing single-cell sortChIC data
lauren-wu/macrogenomics
This is the code for the chromatin packing model in macrogenomics engineering study
LucaUZH/Chromatin-Accessibility-Atlas
Documenation Chromatin Accessibility Atlas
MahShaaban/chromhmmData
chromhmmData: Chromosome Size, Coordinates and Anchor Files
ptrebert/sciddo
Home of the SCIDDO tool
younglab/origami
Statistical Modeling of ChIA-PET interactions
yufanzhouonline/HiSIF
HiSIF: Genome-wide chromatin interactions identify characteristic promoter-distal loops