chromatin-organisation

There are 0 repository under chromatin-organisation topic.

• vaquerizaslab / chess

  Comparison of Hi-C Experiments using Structural Similarity.

  hi-cstructural-similaritycomparative-genomicschromatinchromatin-organisation
  Language:Python 26

• hanjunlee21 / StructuralSimilarity

  Identification of dynamic changes in chromatin conformation is a fundamental task in genetics. In 2020, Galan et al. presented CHESS (Comparison of Hi-C Experiments using Structural Similarity), a novel computational algorithm designed for systematic identification of structural differences in chromatin-contact maps. Using CHESS, the same group recently reported that chromatin organization is largely maintained across tissues during dorsoventral patterning of fruit fly embryos despite tissue-specific chromatin states and gene expression. However, here we show that the primary outputs of CHESS–namely, the structural similarity index (SSIM) profiles–are nearly identical regardless of the input matrices, even when query and reference reads were shuffled to destroy any significant differences. This issue stems from the dominance of the regional counting noise arising from stochastic sampling in chromatin-contact maps, reflecting a fundamentally incorrect assumption of the CHESS algorithm. Therefore, biological interpretation of SSIM profiles generated by CHESS requires considerable caution.

  bioinformaticshi-cchromatin-interactionchromatin-organisationchess
  Language:Python 3

• koustav-pal / HiCBricks

  HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides a R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms.

  hi-chdf5genome-sequencingchromatin-organisationchromatin-structurebioconductor-packagebioconductor-packages
  Language:R 3

• hanjunlee21 / Lee-et-al-2023

  RB represses cohesin-dependent loop formation and safeguards E2F-independent transcription

  bioinformaticscell-cyclechromatin-interactionchromatin-organisationhi-c
  Language:Jupyter Notebook 1
• polymer-model-analyses-of-chromatin-mFISH-data

  Loucif-REMINI / polymer-model-analyses-of-chromatin-mFISH-data

  a tool for the analysis of multiplexed FISH (Fluorescence In Situ Hybridization) data

  biophysicschromatin-organisationdata-analysis-pythonpolymer-physics
  Language:Jupyter Notebook 1

• magnitov / prokaryotic_cids

  The code from the paper "Benchmark of software tools for prokaryotic chromosomal interaction domain identification"

  hi-ccidschromatin-organisation
  Language:Python 1

• rnschmdlr / GAM_project

  WIP. This project aims to quantify the information in genome architecture data. An extensive chromatin toymodel is used for internal method development

  entropychromatin-organisation
  Language:Python 1