Giters

dmattek / burst-calc

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Supplementary code for M Dobrzyński & FJ Bruggeman, Elongation dynamics shape bursty transcription and translation, PNAS, 2009 (link).

Analyze bursts in interarrival times. Last modification: 30 March 2018

Authors: M Dobrzyński, Centre for Mathematics and Computer Science (CWI), Amsterdam, The Netherlands

Content of the directory:

  • burster - C code for Gillespie simulation of the basic burst-generating model
  • slide - C code for Gillespie simulation of motor protein progression along the polymer chain
  • matlab - Matlab scripts
    • mdloghist.m - a Matlab script to produce histograms with logarithmic binning
    • mdburstsz.m - a Matlab script to generate the burst size function
  • R - an Rstudio project
    • calcBurstSzFn.R - an R function to generate the burst size function
    • analyzeBursts.Rmd - an R notebook that demonstrates burst analysis using the example dataset
  • example-data-1 - an example dataset generated with ./burster.x 1 10000 1 0 0.1 0.1 10 1

About

Languages

Language:HTML 82.4%Language:Ruby 15.0%Language:C 2.2%Language:R 0.2%Language:MATLAB 0.2%Language:Makefile 0.1%