README.md

In AnnikaGable/chromium: Analyze and visualize high throughput chromatin interaction data, such as Hi-C or ChIA-PET

chromium

R package for the analysis and visualization of Hi-C data.

• We import preprocessed Hi-C data and convert them into the InteractionSet format (from Bioconductor).
• We provide functions to easily subset the InteractionSet by only the genomic region required, discarding unneccessary genomic annotation to reduce object size.
• The Hi-C data can be binned at any resolution, starting from either binned or restriction fragment resolution data.
• We normalize the interactions using iterative proportional fitting, a matrix balancing algorithm.
• The interactions can be visualized in a triangular visualization alongside ChIPSeq tracks, the genomic axis, etc.

For more info, please visit the package vignette.

AnnikaGable/chromium documentation built on May 5, 2019, 6:04 a.m.