scripts and supplementary files for a study on modeling whole genome DSB profiles with chromatin features.
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figures
notebooks
scripts
.gitignore
NOTES.get_cancer_svcnts
NOTES.make_chromHMM_states
NOTES_I.make_features_matrices
NOTES_II.make_input_dsb_data
NOTES_III.make_RF_models
NOTES_IV.make_dscores
NOTES_IVa.correct_loci
NOTES_V.make_circperm_data
README
Supplementary_Tables1-2.xlsx
annotations.list
hg19_50kb_bins.bed
hg19_chr.lengths
opensource_license

README

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# README for DSB model study 
This is a collections of scripts for doing the analysis in "Modelling double strand break susceptibility to interrogate structural variation in cancer" by Ballinger and Bouwman et al. 

The NOTES_*.* files describe and contain commands for running the analysis described in the paper.  They are ordered chronologically to match the flow of the manuscript and build upon each other.  

scripts/ contains scripts used to do the analysis, which are referenced in the NOTES files. 
notebooks/ contains iPython notebooks with the R commands used to generate the figures for the manuscript. 
figures/ contains the figures that went in the manuscript. 

Data files can be found at XXX, which contains a link to data.tar.gz file.  This archive contains all supplementary data files for the manuscript.