- hicexplorer hicmergematrixbins
Merges bins from a Hi-C matrix.
- hicexplorer hicplotmatrix
Creates a heatmap of a Hi-C matrix
- hicexplorer hiccorrectmatrix-correct
Run Knight-Ruiz matrix balancing algorithm (KR) or the iterative matrix correction (ICE)
- hicexplorer hiccorrectmatrix-diagnostic-plot
This function provides 2 balancing methods which can be applied on a raw matrix.
- hicexplorer hicbuildmatrix
Using an alignment from a program that supports local alignment (eg. Bowtie2) where both PE reads are mapped using the –local option, this program reads such file and creates a matrix of interactions.
- hicexplorer hicfindtads
Uses a measure called TAD-separation score to identify the degree of separation between the left and right regions at each Hi-C matrix bin. This is done for a running window of different sizes. Then, TADs are called as those positions having a local TAD-separation score minimum.
- hicexplorer hicsummatrices
Adds Hi-C matrices of the same size. Format has to be hdf5 (.h5) or npz
- hicexplorer hicdetectloops
hicDetectLoops can detect enriched interaction regions (peaks / loops) based on a strict candidate selection, negative binomial distributions and Wilcoxon rank-sum tests.