Projects in Awesome Lists tagged with chromatin-interaction

A curated list of projects in awesome lists tagged with chromatin-interaction .

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https://github.com/aryeelab/hichipper

A preprocessing and QC pipeline for HiChIP data

bioinformatics chromatin-interaction epigenetics hichip

Last synced: 11 Mar 2026

https://github.com/bioinfomaticscsu/looppredictor

LoopPredictor: Predicting unknown enhancer-mediated genome topology by an ensemble machine learning model

chromatin-interaction classifying-loops conda-environment predicting-loops

Last synced: 12 Mar 2026

https://github.com/ibn-salem/sevenc

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

3d-genome chip-seq chromatin-interaction hi-c prediction r-package sequence-motif transcription-factors

Last synced: 18 Feb 2026

https://github.com/pasquali-lab/umi4cats

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

chromatin chromatin-interaction genomics umi4c

Last synced: 19 Feb 2026

https://github.com/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.

bioinformatics chess chromatin-interaction chromatin-organisation hi-c

Last synced: 30 Apr 2025