ArticleBioinformatics (Oxford, England)2023
IsoTools: a flexible workflow for long-read transcriptome sequencing analysis.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- To be or not to be a protein coding mutation, that's the question!NAR genomics and bioinformatics · 2025Review
- Long-read sequencing transcriptome quantification with lr-kallisto.PLoS computational biology · 2025Article
- Investigating RNA dynamics from single molecule transcriptomes.Trends in genetics : TIG · 2025Review
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq.Genome research · 2025Article
- Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads.Genome research · 2025Article
- Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation.Genome research · 2025Review
- Discovery of Novel Protein-Coding and Long Non-coding Transcripts in Distinct Regions of the Human Brain.Journal of molecular neuroscience : MN · 2025Article
- TrAnnoScope: A Modular Snakemake Pipeline for Full-Length Transcriptome Analysis and Functional Annotation.Genes · 2024Article
- Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects ofGenome research · 2024Article
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments.bioRxiv : the preprint server for biology · 2024Article
- Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation.Molecular systems biology · 2024Article
- Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.Nature methods · 2024Article
- Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data.Nature communications · 2024Article
- Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD.Nucleic acids research · 2024Article
- Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.bioRxiv : the preprint server for biology · 2023Article
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8 authors.
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Abstract
motivationLong-read transcriptome sequencing (LRTS) has the potential to enhance our understanding of alternative splicing and the complexity of this process requires the use of versatile computational tools, with the ability to accommodate various stages of the workflow with maximum flexibility.
resultsWe introduce IsoTools, a Python-based LRTS analysis framework that offers a wide range of functionality for transcriptome reconstruction and quantification of transcripts. Furthermore, we integrate a graph-based method for identifying alternative splicing events and a statistical approach based on the beta-binomial distribution for detecting differential events. To demonstrate the effectiveness of our methods, we applied IsoTools to PacBio LRTS data of human hepatocytes treated with the histone deacetylase inhibitor valproic acid. Our results indicate that LRTS can provide valuable insights into alternative splicing, particularly in terms of complex and differential splicing patterns, in comparison to short-read RNA-seq. AVAILABILITY AND IMPLEMENTATION: IsoTools is available on GitHub and PyPI, and its documentation, including tutorials, CLI, and API references, can be found at https://isotools.readthedocs.io/.
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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 Socratic graph.