ArticleBioinformatics (Oxford, England)2015
Polyester: simulating RNA-seq datasets with differential transcript expression.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 181 papers, 1 of them a synthesis that pooled it.
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Who cites it
181 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of RNA sequencing datasets reveals an association between TRAJ23, psoriasis, and IL-17A.JCI insight · 2018Pooled it
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- Comprehensive assessment of transcriptome assembly quality using CATS.Nature communications · 2026Article
- Improving gene isoform quantification with miniQuant.Nature biotechnology · 2026Article
- Eduomics: a Nextflow pipeline to simulate -omics data for education.NAR genomics and bioinformatics · 2026Article
- AQUARIUM_HB: a bioinformatics pipeline for human blood circular RNA analysis.Non-coding RNA research · 2026Article
- Bayesian reconstruction and differential testing of excised introns.Bioinformatics (Oxford, England) · 2025Article
- Tree-based differential testing using inferential uncertainty for RNA-seq.Genome research · 2025Article
- Widespread 3' UTR splicing regulates expression of oncogene transcripts through multiple mechanisms.Nucleic acids research · 2025Article
- Anchorage accurately assembles anchor-flanked synthetic long reads.Algorithms for molecular biology : AMB · 2025Article
- DOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction reads.Nature communications · 2025Article
- NGPINT V3: a containerized orchestration Python software for discovery of next-generation protein-protein interactions.Bioinformatics (Oxford, England) · 2025Article
- A novel splicing graph allows a direct comparison between exon-based and splice junction-based approaches to alternative splicing detection.Briefings in bioinformatics · 2025Article
- A new Similarity Based Adapted Louvain Algorithm (SIMBA) for active module identification in p-value attributed biological networks.Scientific reports · 2025Article
- Tree-based differential testing using inferential uncertainty for RNA-Seq.bioRxiv : the preprint server for biology · 2025Article
121 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationStatistical 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.
resultsPolyester is an R package designed to simulate RNA-seq data, beginning with an experimental design and ending with collections of RNA-seq reads. Its main advantage is the ability to simulate reads indicating isoform-level differential expression across biological replicates for a variety of experimental designs. Data generated by Polyester is a reasonable approximation to real RNA-seq data and standard differential expression workflows can recover differential expression set in the simulation by the user. AVAILABILITY AND IMPLEMENTATION: Polyester is freely available from Bioconductor (http://bioconductor.org/). CONTACT: jtleek@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.