Welcome to HiC sunt dracones (or HiCSD in short).
The functions of HiCsd are built on both Hi-C Pro matrices and Homer matrices. HiCsd uses HiCUP for truncation and filtering of reads and implicit matrix normalization (ICEing) as implemented Hi-C Pro. It is further possible, to explicitly normalize read counts of certain regions in the raw matrix for relative differences in ploidy. HiCsd then allows to analyse the full HiC matrix, differential matrices, a desired subset of a matrix (submatrix) as well as individual chromosomes. These matrices can be visualized either as full heatmaps or triangles with color and scale of the heatmaps adjustable. Using HiCsd, testing colocalization of loci of interest is easy as HiCsd can pick these loci from a genome annotation by searching for given keywords or by feeding a list of loci of interest into the program. Also, HiCsd is able to compare the interaction frequencies of distinct loci between different matrices. The distance dependent decay of interaction frequencies can be calculated for both, individual chromosomes or as a mean/median function including all chromosomes of choice. Also, HiCsd is able to extract the interaction frequencies between any locus of choice with all other genomic loci, thus generating 4C-like profiles in wiggle format, that can easily be explored and compared using a common genome browser.
usage: hicsd [-h] {version} ...
positional arguments:
{version} commands
version Show version
optional arguments:
-h, --help show this help message and exit
usage: hicsd [-h]
{version,hicpro2homer,number_of_bins,chromosomes,norm_by_col_sum,submatrix,diff_matrix,heatmap,virtual_4C,dist_dep_decay,colo,colo_diff}
...
positional arguments:
{version,hicpro2homer,number_of_bins,chromosomes,norm_by_col_sum,submatrix,diff_matrix,heatmap,virtual_4C,dist_dep_decay,colo,colo_diff}
commands
version Show version
hicpro2homer Convert a matrix in HiC-Pro format to Homer format
number_of_bins Return the number of bins of the matrix
chromosomes Return the chromosomes used in the matrix
norm_by_col_sum Normalize by column sum to make matrices comparable
submatrix Extract submatrices
diff_matrix Generate differential matrix by dividing the values of
one matrix by the values of the other.
heatmap Plot interaction matix heatmap
virtual_4C Perform virtual 4C analysis
dist_dep_decay Distant dependent decay
colo Perform colocalisation analysis
colo_diff Perform differential colocalisation analysis
optional arguments:
-h, --help show this help message and exit
This repo contains 2 branches: "master" for development and "production" for stable releases