Topic: chromatin Goto Github
Some thing interesting about chromatin
Some thing interesting about chromatin
chromatin,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
Organization: 3dgenomes
chromatin,3D Genome Browser
Organization: 3dgenomes
Home Page: https://3dgenomes.github.io/TADkit/
chromatin,Benchmarking simulation frameworks for chromatin folding. (https://resgen.io/l/?d=IBvynlJsQ5qMAvSa9JP3XQ)
Organization: 4dn-hack-team9-2024
chromatin,Chromatin loop caller using Topological Data Analysis based on Hi-C data
User: aleskunder
chromatin,ChIPseq pipeline for Pasini's lab written in snakemake
User: andreamariani-am
chromatin,Sample Analysis for diffloop paper
Organization: aryeelab
chromatin,Code to model active loop extrusion on chromatin using hybrid MD-MC.
User: bchan-4
Home Page: https://www.pnas.org/doi/10.1073/pnas.2401494121
chromatin,Multi Resolution Analysis of Tiling Arrays. (R package)
User: benja0x40
chromatin,ChIP-seq normalization according to background reads density. (R package)
User: benja0x40
chromatin,Workflow for processing single-cell sortChIC data
Organization: bhardwaj-lab
chromatin,Super-resolution chromatin tracing 2018
User: bogdanbintu
chromatin,ChromaSEP
User: eguarnera
chromatin,ChromaWalker
User: eguarnera
chromatin,CUT&RUN and CUT&Tag data processing and analysis
User: fl-yu
chromatin,Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.
User: gryderart
chromatin,Multiple-replica multiple-condition Macs2 ChIPSeq wrapper
Organization: huntsmancancerinstitute
chromatin,This is the code for the chromatin packing model in macrogenomics engineering study
User: lauren-wu
chromatin,Documenation Chromatin Accessibility Atlas
User: lucauzh
chromatin,chromhmmData: Chromosome Size, Coordinates and Anchor Files
User: mahshaaban
Home Page: https://www.bioconductor.org/packages/chromhmmData/
chromatin,Methods for summarizing and visualizing multi-biosample functional genomic annotations
User: meuleman
Home Page: https://epilogos.net
chromatin,🖥️📚 WorkflowR site containing code and analyses produced throghout my PhD thesis.
User: mireia-bioinfo
Home Page: https://mireia-bioinfo.github.io/phdthesis_code/
chromatin,A cool place to store your Hi-C
Organization: open2c
Home Page: https://open2c.github.io/cooler
chromatin,Chromosome polymer simulations and in silico capture experiments
Organization: open2c
chromatin,An R package for analyzing UMI-4C chromatin contact data.
Organization: pasquali-lab
Home Page: https://pasquali-lab.github.io/UMI4Cats/
chromatin,Make a phylogeny using the chromatin structure information extracted from Hi-C experiments (mirror of the original repo)
User: picani
Home Page: https://gite.lirmm.fr/pulicani/phyloHiC
chromatin,Reconstruction of 3D conformation of chromatin fiber using single cell Hi-C data
User: polly-code
chromatin,Processing, quality control and analysis of GAM datsets
Organization: pombo-lab
Home Page: http://gam.tools
chromatin,Home of the SCIDDO tool
User: ptrebert
chromatin,Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data
User: raevskymichail
chromatin,Step-by-step instructions and Snakemake pipeline for processing Cut&Run data
Organization: sansamlab-pipelines-genomics
chromatin,ChIP-seq pipeline specific for the Zwart lab
User: sebastian-gregoricchio
chromatin,C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
User: tanjimin
chromatin,Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
User: tobiasrausch
Home Page: https://tobiasrausch.com/courses/atac/
chromatin,Scripts to create cartoons of 3D genomes
User: tzeitim
chromatin,Comparison of Hi-C Experiments using Structural Similarity.
Organization: vaquerizaslab
chromatin,A Python implementation for BH-FDR and HiCCUPS
User: xiaotaowang
chromatin, A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
User: xiaotaowang
chromatin,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.
User: youssefayachii
chromatin,HiSIF: Genome-wide chromatin interactions identify characteristic promoter-distal loops
User: yufanzhouonline
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