Helper scripts for pre-processing Hi-C to deepC input, as well as helper for visualization and analysis.
example_head_10lines_data_K562_5kb_regression.txt- example file including 10 lines demonstrating how to prepare Hi-C data for input to the deepC training script.- Format: chr start stop percentile_tags (comma separated)
- each region is a 1 Mb + 1x bin_size region
- the comma separated percentile tags correspond to the normalized Hi-C interaction values over the center of that region
- regions are incremented in bin_size steps.
functions_for_deepC- R functions for preprocessing Hi-C data to deepC format and helper for analysing and visualizing deepC predictions e.g.: compare reference vs. variant predictions- virtual4C
functions_for_HiC.R- general helper functions for loading, processing and visualising Hi-C data (copy from here)- reference_manual detailing all available functions.
match_query_table.pl- helper perl script for processing Hi-C datamatch_query_table.pl- helper perl script for processing Hi-C data
Some R functions require a working version of bedtools being installed and available in your standard path as queried from within R. Uses "bedtools makewindows".
Some R functions require a working version of perl being installed and available in your standard path as queried from within R.
Requires a recent version of "tidyverse" and "RColorBrewer".