Revealing Hi-C subcompartments by imputing inter-chromosomal ... - Nature
2019年11月7日 · Here we develop a computational approach, SNIPER (Subcompartment iNference using Imputed Probabilistic ExpRessions), based on denoising autoencoder and multilayer perceptron classifier to infer...
scGHOST: identifying single-cell 3D genome subcompartments
2024年4月8日 · Using scHi-C data from complex tissues, scGHOST identifies cell-type-specific or allele-specific subcompartments linked to gene transcription across various cell types and developmental stages,...
Hi-C：染色质高维数据可视化与读图逻辑_et - 搜狐
2019年3月17日 · Subcompartment： 细胞核隔间，在三维构象Models里面展示为染色质的团块结构；在Matrices展示为一定面积具有颜色深度的色块。 Ordinary Dormain： 在 Matrices模式里面的为单一色块单元，对应Models模块里面的一个染色质高级结构域单元。
Systematic inference and comparison of multi-scale chromatin sub ...
2021年5月10日 · Calder allows to infer and compare chromatin sub-compartments and compartment domains in >100 cell lines. Our results reveal sub-compartments enriched for poised chromatin states and undergoing...
Identification of Two Subsets of Subcompartment A1 Associated …
2023年7月27日 · Here, we first utilized genome-wide Hi-C data to infer eight types of subcompartment (labeled A1, A2, A3, A4, B1, B2, B3, and B4) in mouse embryonic stem cells and four primary differentiated cell types, including thymocytes, macrophages, neural progenitor cells, and cortical neurons.
dcHiC: Differential Compartment Analysis of Hi-C Datasets - GitHub
2022年11月11日 · The differential loop files list significant loop interactions and their associated differential compartment anchors, whereas the subcompartment files illustrate HMM-segmented subcompartments based on the magnitude of the PC values. Below is a diagram of the overarching results structure, containing two different runs
Formation of Chromatin Subcompartments by Phase Separation
2018年5月22日 · In addition to cooperative binding of proteins to a preformed chromatin structure, two different mechanisms for the formation of phase-separated chromatin subcompartments have been proposed. One is based on bridging proteins that cross-link polymer segments with particular properties.
Approaches to characterize chromatin subcompartment …
2023年12月1日 · Here we review recent approaches to measure features of chromatin subcompartments (CSCs) that have dimensions on the 100 nm to μm scale and involve the assembly of protein/RNA macromolecules around certain chromatin loci.
GitHub - ma-compbio/scGHOST: single-cell Hi-C, scHi-C, Hi-C, 3D …
scGHOST is an unsupervised single-cell subcompartment annotation method based on graph embedding with constrained random walk sampling. scGHOST is designed to be run on a single-cell Hi-C (scHi-C) dataset which has undergone imputation by Higashi (Zhang et al. 2022). scGHOST assigns embeddings to genomic loci in the genomes of individual cells ...
Systematic inference and comparison of multi-scale chromatin sub ...
2021年5月10日 · Here, we present Calder, an algorithmic approach that enables the identification of multi-scale sub-compartments at variable data resolution. Calder allows to infer and compare chromatin sub-compartments and compartment domains in >100 cell lines.