iceDP 1.0.0

Identify inter-chromatin interaction utilize density peaks algorithm

iceDP project description

Installation

Way one

copy to ${python_path}/site-packages

Way two

    pip install iceDP  # not up load yet

Usage

• Data required

iceDP receive any genome interaction data in a three-column format as input. Before running analyses, we need to prepare genome interaction data in a three-column format:

Column 1 (chr_one_site) → Genomic position on the first chromosome.

Column 2 (chr_two_site) → Genomic position on the second chromosome.

Column 3 (interaction_value) → Interaction strength between the two positions (typically observed in Hi-C experiments).

Check the sample data:

head -5 play_data/chr4_chr11_mm10.txt
3090000 3100000 1.0
3795000 3100000 1.0
4205000 3100000 1.0
4255000 3100000 1.0
4230000 3105000 1.0

This file represents genomic interactions between chromosome 4 and chromosome 11 in the mouse genome (mm10).

If your data is stored in .hic format, you can extract interaction values using Juicer Tools:

java -jar juicer_tools.jar dump observed NONE mydata.hic chr4 chr11 BP 50000 chr4_chr11_mm10.txt

Juicer Tools can be fetch from: https://github.com/aidenlab/juicertools

• iceDP procedure

    import iceDP

    x=iceDP.main_procedure.bunchDots()
    x.readData('play_data/chr4_chr11_mm10.txt')
    x.get_rho()    # calculate rho
    x.get_delta()  # calculate delta
    x.do_chi_square_test()
    x.define_border()
    x.horizontal_and_vertical_fold_change()
    iceDP.main_procedure.save_reult(x, 'chr4_chr11_mm10_DPresult')  # save result

• plot

    iceDP.plot_spots.plot_one_spot(x.data_filted2.values[1], x)