VSS-Hi-C: variance-stabilized signals for chromatin contacts.

ABSTRACT:

Motivation

The genome-wide chromosome conformation capture assay Hi-C is widely used to study chromatin 3D structures and their functional implications. Read counts from Hi-C indicate the strength of chromatin contact between each pair of genomic loci. These read counts are heteroskedastic: that is, a difference between the interaction frequency of 0 and 100 is much more significant than a difference between the interaction frequency of 1000 and 1100. This property impedes visualization and downstream analysis because it violates the Gaussian variable assumption of many computational tools. Thus heuristic transformations aimed at stabilizing the variance of signals like the shifted-log transformation are typically applied to data before its visualization and inputting to models wit

SUBMITTER: Kenari NS 

PROVIDER: S-EPMC11648998 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature