ArticleNucleic acids research2014
PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 42 citations in OpenAlex.
- Integrative analysis via bioinformatics and machine learning identifies SERPING1 as a biomarker candidate for major depressive disorder.BMC psychiatry · 2026Article
- Application of Single-Cell RNA Sequencing in Ovarian Development.Biomolecules · 2022Review
- Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision.Briefings in bioinformatics · 2021Article
- LIQA: long-read isoform quantification and analysis.Genome biology · 2021Article
- LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.BMC genomics · 2020Article
- Strategies for eQTL mapping in allopolyploid organisms.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- PennDiff: detecting differential alternative splicing and transcription by RNA sequencing.Bioinformatics (Oxford, England) · 2018Article
- Article
- Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates.PLoS computational biology · 2017Article
- Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways.Cell systems · 2016Article
- The exon quantification pipeline (EQP): a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data.Nucleic acids research · 2016Article
- DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics.F1000Research · 2016Article
- Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data.Bioinformatics (Oxford, England) · 2015Article
- MetaDiff: differential isoform expression analysis using random-effects meta-regression.BMC bioinformatics · 2015Article
- Integration of disease association and eQTL data using a Bayesian colocalisation approach highlights six candidate causal genes in immune-mediated diseases.Human molecular genetics · 2015Article
- WemIQ: an accurate and robust isoform quantification method for RNA-seq data.Bioinformatics (Oxford, England) · 2015Article
- Article
- Mapping Splicing Quantitative Trait Loci in RNA-Seq.Cancer informatics · 2015Article
- Mapping Splicing Quantitative Trait Loci in RNA-Seq.Cancer informatics · 2014Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
Correctly estimating isoform-specific gene expression is important for understanding complicated biological mechanisms and for mapping disease susceptibility genes. However, estimating isoform-specific gene expression is challenging because various biases present in RNA-Seq (RNA sequencing) data complicate the analysis, and if not appropriately corrected, can affect isoform expression estimation and downstream analysis. In this article, we present PennSeq, a statistical method that allows each isoform to have its own non-uniform read distribution. Instead of making parametric assumptions, we give adequate weight to the underlying data by the use of a non-parametric approach. Our rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution. We evaluate the performance of PennSeq using both simulated data with known ground truth, and using two real Illumina RNA-Seq data sets including one with quantitative real time polymerase chain reaction measurements. Our results indicate superior performance of PennSeq over existing methods, particularly for isoforms demonstrating severe non-uniformity. PennSeq is freely available for download at http://sourceforge.net/projects/pennseq.
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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.