vssHiC is an extension of the VSS, a signal transformation approach used for variance stabilization of epigenomic signals to support
Hi-C modality. Genome-wide chromatin conformation capture assay, Hi-C, allows studying chromatin 3D structural features
and their functional implications, but the variance instability of raw read counts hinders the visualization and downstream analysis of this data modality. vssHiC stabilizes
the variance of signals across a dynamic range, makes heatmap visualization of contact maps more appealing, and improves the performance of subcompartment callers
relying on Gaussian observed variables. vssHiC is compatible with a well-developed R class InteractionSet and file format .cool for Hi-C data. There are also
wrapper functions implemented for three TAD callers to support InteractionSet object and output TAD domains as a GRanges object which can be easily visualized on top of the
heatmap of Hi-C contact maps by the HiContacts package.
You can install the development version of vssHiC from Github:
library(devtools)
devtools::install_github("nedashokraneh/vssHiC")A vignette of the vssHiC manual is provided at https://rpubs.com/nshokran/vssHiC.
Neda Shokraneh Kenari, Faezeh Bayat, Maxwell Libbrecht. VSS-Hi-C: Variance-stabilized signals for chromatin contacts. bioRxiv 2021.10.19.