@article {Frazee006015, author = {Alyssa C. Frazee and Andrew E. Jaffe and Ben Langmead and Jeffrey T. Leek}, title = {Polyester: simulating RNA-seq datasets with differential transcript expression}, elocation-id = {006015}, year = {2014}, doi = {10.1101/006015}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Statistical methods development for differential expression analysis of RNA sequencing (RNA-seq) requires software tools to assess accuracy and error rate control. Since true differential expression status is often unknown in experimental datasets, artificially-constructed datasets must be utilized, either by generating costly spike-in experiments or by simulating RNA-seq data. Polyester is an R package designed to simulate RNA-seq data, beginning with an experimental design and ending with collections of RNA-seq reads. The main advantage of Polyester is the ability to simulate isoform-level differential expression across biological replicates for a variety of experimental designs at the read level. Differential expression signal can be simulated with either built-in or user-defined statistical models. Polyester is available on GitHub at https://github.com/alyssafrazee/polyester.}, URL = {https://www.biorxiv.org/content/early/2014/06/06/006015}, eprint = {https://www.biorxiv.org/content/early/2014/06/06/006015.full.pdf}, journal = {bioRxiv} }