chromatin
There are 1 repository under chromatin topic.
- HiC_tools
- Language:Python 201
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
Language:Python 100fl-yu / CUT-RUNTools-2.0
CUT&RUN and CUT&Tag data processing and analysis
Language:Shell 93tobiasrausch / ATACseq
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
Language:Shell 74tanjimin / C.Origami
C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
Language:Python 60- Language:R 58
- Language:Python 46
meuleman / epilogos
Methods for summarizing and visualizing multi-biosample functional genomic annotations
Language:Python 41XiaoTaoWang / HiCPeaks
A Python implementation for BH-FDR and HiCCUPS
Language:Python 41A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
Language:Python 39- Language:JavaScript 31
vaquerizaslab / chess
Comparison of Hi-C Experiments using Structural Similarity.
Language:Python 26- Language:Nextflow 20
BogdanBintu / ChromatinImaging
Super-resolution chromatin tracing 2018
Language:Jupyter Notebook 14tzeitim / genome-blender
Scripts to create cartoons of 3D genomes
Language:Python 13GryderArt / AQuA-HiChIP
Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.
Language:R 11- Language:Python 9
HuntsmanCancerInstitute / MultiRepMacsChIPSeq
Multiple-replica multiple-condition Macs2 ChIPSeq wrapper
Language:Perl 7- UMI4Cats
Pasquali-lab / UMI4Cats
An R package for analyzing UMI-4C chromatin contact data.
Language:R 5 raevskymichail / epi-impute
Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data
Language:R 5SansamLab-Pipelines-Genomics / Cut_And_Run_Analysis_SnakeMake
Step-by-step instructions and Snakemake pipeline for processing Cut&Run data
Language:Python 5- Language:Python 4
- topology_loop_caller
aleskunder / topology_loop_caller
Chromatin loop caller using Topological Data Analysis based on Hi-C data
Language:Python 3 polly-code / DPDchrom
Reconstruction of 3D conformation of chromatin fiber using single cell Hi-C data
Language:Fortran 3- Language:Perl 3
mireia-bioinfo / phdthesis_code
🖥️📚 WorkflowR site containing code and analyses produced throghout my PhD thesis.
Language:HTML 2YoussefAyachii / 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
Language:Python 1lauren-wu / macrogenomics
This is the code for the chromatin packing model in macrogenomics engineering study
Language:Python 1LucaUZH / Chromatin-Accessibility-Atlas
Documenation Chromatin Accessibility Atlas
Language:Jupyter Notebook 1MahShaaban / chromhmmData
chromhmmData: Chromosome Size, Coordinates and Anchor Files
- Language:Python 1
- Language:Shell 1
yufanzhouonline / HiSIF
HiSIF: Genome-wide chromatin interactions identify characteristic promoter-distal loops
Language:C++ 1
