HiC sunt dracones - Your little helper for HiC analyses

Welcome to HiC sunt dracones (or HiCSD in short).

Why should you use HiC sunt dracones?

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.

Subcommand overview

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

Development

This repo contains 2 branches: "master" for development and "production" for stable releases

Trivia

• Origin of the name