chromatin

There are 50 repositories under chromatin topic.

  • HiC_tools

    mdozmorov/HiC_tools

    A collection of tools for Hi-C data analysis

    556366125

  • open2c/cooler

    A cool place to store your Hi-C

    Language:Python2091429852

  • mdozmorov/HiC_data

    A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

    17713230

  • fl-yu/CUT-RUNTools-2.0

    CUT&RUN and CUT&Tag data processing and analysis

    Language:Shell10137655

  • 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:Python1001725461

  • tobiasrausch/ATACseq

    Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

    Language:Shell747636

  • tanjimin/C.Origami

    C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

    Language:Python674279

  • ay-lab/dcHiC

    dcHiC: Differential compartment analysis for Hi-C datasets

    Language:R6459710

  • open2c/polychrom

    Chromosome polymer simulations and in silico capture experiments

    Language:Python4792116

  • XiaoTaoWang/HiCPeaks

    A Python implementation for BH-FDR and HiCCUPS

    Language:Python43299

  • meuleman/epilogos

    Methods for summarizing and visualizing multi-biosample functional genomic annotations

    Language:Python423245

  • XiaoTaoWang/TADLib

    A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

    Language:Python4032711

  • 3DGenomes/TADkit

    3D Genome Browser

    Language:JavaScript31174410

  • vaquerizaslab/chess

    Comparison of Hi-C Experiments using Structural Similarity.

    Language:Python264586

  • aertslab/PUMATAC

    Pipeline for Universal Mapping of ATAC-seq

    Language:Nextflow24411

  • BogdanBintu/ChromatinImaging

    Super-resolution chromatin tracing 2018

    Language:Jupyter Notebook14725

  • tzeitim/genome-blender

    Scripts to create cartoons of 3D genomes

    Language:Python13205

  • GryderArt/AQuA-HiChIP

    Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.

    Language:R11304

  • pombo-lab/gamtools

    Processing, quality control and analysis of GAM datsets

    Language:Python921014

  • HuntsmanCancerInstitute/MultiRepMacsChIPSeq

    Multiple-replica multiple-condition Macs2 ChIPSeq wrapper

    Language:Perl7501
  • UMI4Cats

    Pasquali-lab/UMI4Cats

    An R package for analyzing UMI-4C chromatin contact data.

    Language:R52153

  • raevskymichail/epi-impute

    Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data

    Language:R5313

  • SansamLab-Pipelines-Genomics/Cut_And_Run_Analysis_SnakeMake

    Step-by-step instructions and Snakemake pipeline for processing Cut&Run data

    Language:Python50134

  • gtca/chame

    Chromatin analysis module

    Language:Python4200
  • topology_loop_caller

    aleskunder/topology_loop_caller

    Chromatin loop caller using Topological Data Analysis based on Hi-C data

    Language:Python3231

  • polly-code/DPDchrom

    Reconstruction of 3D conformation of chromatin fiber using single cell Hi-C data

    Language:Fortran3210

  • younglab/fourfold

    4C-seq data processing and visualization pipeline

    Language:Perl3300

  • mireia-bioinfo/phdthesis_code

    🖥️📚 WorkflowR site containing code and analyses produced throghout my PhD thesis.

    Language:HTML2202

  • 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.

    2100

  • bhardwaj-lab/scChICflow

    Workflow for processing single-cell sortChIC data

    Language:Python1120

  • lauren-wu/macrogenomics

    This is the code for the chromatin packing model in macrogenomics engineering study

    Language:Python1300

  • LucaUZH/Chromatin-Accessibility-Atlas

    Documenation Chromatin Accessibility Atlas

    Language:Jupyter Notebook1100

  • MahShaaban/chromhmmData

    chromhmmData: Chromosome Size, Coordinates and Anchor Files

    120

  • nf-core/sammyseq

    Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.

    Language:Nextflow1158144

  • ptrebert/sciddo

    Home of the SCIDDO tool

    Language:Python1251

  • yufanzhouonline/HiSIF

    HiSIF: Genome-wide chromatin interactions identify characteristic promoter-distal loops

    Language:C++1230