This repository contains code used to produce the results in the paper "Genome-wide modelling of transcription kinetics reveals patterns of RNA processing delays".

All code is available under the BSD license (see LICENSE.txt).

The GP code is implemented in Matlab and uses the GPmat library (https://github.com/SheffieldML/GPmat).

The main script for running the code is 'matlab/run_all_gpnddisim_hmc_convcheck_mixprior.m' for the real data and 'matlab/run_all_gpnddisim_hmc_convcheck_mixprior_synthetic.m' for the synthetic data.

The scripts make assumptions about file names and locations so they would need editing before running.

There is a number of Matlab scripts for post-processing the HMC samples: 'matlab/check_early_profiles.m' 'matlab/combine_profiles.m' 'matlab/analyse_hmc_new.m' 'matlab/get_hmc_medians_new.m'

The scripts make assumptions about file names and locations so they would need editing before running.

The main entry point is 'matlab/run_plot_sampled_predictions.m'.

The analysis code is written in R. The main script is 'R/analyse_intron_lengths_meddelay.R'. The script run the analysis and writes most of the figures in the paper.

The code is written in Python and is at 'python/plotwigs.py'.

Pol-II pre-processing code is in 'matlab/pol2_processing'. RNA-seq pre-processing code is in 'matlab/rnaseq_processing'.