ASimulatoR: splice-aware RNA-Seq data simulation
Quirin Manz, Olga Tsoy, Amit Fenn, Jan Baumbach, Uwe Völker, Markus List, Tim Kacprowski
Abstract
SUMMARY: A plethora of tools exist for RNA-Seq data analysis with a focus on alternative splicing (AS). However, appropriate data for their comparative evaluation is missing. The R package ASimulatoR simulates gold standard RNA-Seq datasets with fine-grained control over the distribution of AS events, which allow for evaluating alternative splicing tools, e.g. to study the effect of sequencing depth on the performance of AS event detection. AVAILABILITY AND IMPLEMENTATION: ASimulatoR is freely available at https://github.com/biomedbigdata/ASimulatoR as an R package under GPL-3 license.
Topics & Concepts
RNA-SeqspliceComputer scienceRNA splicingComputational biologySoftwareRNAProgramming languageBiologyTranscriptomeGeneticsGeneGene expressionRNA Research and SplicingRNA modifications and cancerCancer-related molecular mechanisms research