Scott Ronquist, scotronq@umich.edu. 1/18/19
The 4DNvestigator is a MATLAB toolbox that analyzes time-series genome-wide chromosome conformation capture (Hi-C) and gene expression (RNA-seq) data.
Paper: in preparation
Availability: https://github.com/scotronq/4DNvestigator
the 4DNvestigator accepted the following input file formats:
| Data Type | File Type | Program |
|---|---|---|
| Hi-C | .hic | Juicer |
| RNA-seq | .genes.results | RSEM |
- Larntz-Perlman procedure: Method for testing the equality of correlation matrices. This is applied to Hi-C correlation matrices to determine the significance of matrix differences.
- von Neuman entropy: Measures the entropy ("uncertainty") of a multivariate system. Uncertainty is related to stemness. Here, we use this measure to determine stemness of Hi-C samples.
- Chromatin partitioning: Partitioning of the genome into two distinct groups based on either the Fiedler vector or principal component 1. This partitioning corresponds to euchromatin and heterochromatin, or A/B compartments.
- Differential expression: Differential expression measures the significance of RNA-seq expression differences between samples.
- 4DN Feature Analyzer: This measures the amount of change in both genome structure and function for specified genomic regions by mapping all time points to a consistent low dimensional embedding, and quantifying the variance of each loci within this space over time. Method specifics can be found in: "Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming"
- A/B switching: This function determines which genomic regions change their chromatin structure from compartment "A" to compartment "B"