CHANGES IN VERSION 1.7.2, 23 January 2016: * Fixes bug where extra keyword-arguments passed to simulate_experiment when using a GTF file would cause an error. CHANGES IN VERSION 1.7.1, 17 November 2015: * Now supports writing more than 1 million reads by chunks. Changes implemented by Rory Kirchner and verified by Leonardo Collado-Torres. CHANGES IN VERSION 1.2.3, 31 March 2015: * change URL of example chromosome 22 sequence dataset / do not test internet-connectivity-dependent stuff during check CHANGES IN VERSION 1.2.2, 9 March 2015: * bug fix in fragment start position simulation with positional bias CHANGES IN VERSION 1.2.1, 14 January 2015: * major refactor: - reduced number of arguments for wrapper functions (simulate_experiment and simulate_experiment_countmat) - shortened source code in wrapper functions by adding several internal helper functions * several new features added: - GC bias in expression - empirical fragment length distribution model available - positional bias in fragmentation step - empirical error models available - custom library size factors available - simulate_experiment_empirical function added as quick way to simulate an experiment with abundances derived from a data set CHANGES IN VERSION 1.99.3, 5 December 2014: * NB function now exported * note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor. CHANGES IN VERSION 1.99.2, 16 November 2014: * bug fix in fragment generation (last 2 bases of transcript were never sequenced) CHANGES IN VERSION 1.99.0; tiny fixes in version 1.99.1. Version 0.99.1 became release version 1.0.0. CHANGES IN VERSION 0.99.1, 22 September 2014: * fixed bug where read names were incorrect in output fasta files * updated vignette * added biocViews * fixed coding style Package submission, version 0.99.0, 18 July 2014