ArticleBMC bioinformatics2014
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.Nature communications · 2026Article
- Full-length transcriptomic profiling reveals age-associated isoform remodeling and altered coding potential in the mouse ovary.Journal of ovarian research · 2026Article
- mRNA splicing in turkey muscle satellite cells is dynamically altered upon thermal challenge.PloS one · 2026Article
- Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.bioRxiv : the preprint server for biology · 2025Article
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Epstein-Barr virus induces host shutoff extensively via BGLF5-independent mechanisms.Cell reports · 2024Article
- H3.3-G34W in giant cell tumor of bone functionally aligns with the exon choice repressor hnRNPA1L2.Cancer gene therapy · 2024Article
- A multiomic atlas of the aging hippocampus reveals molecular changes in response to environmental enrichment.Nature communications · 2024Article
- Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2024Article
- Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons.Genome biology · 2024Article
- An in vitro neurogenetics platform for precision disease modeling in the mouse.Science advances · 2024Article
- Isoform alterations in the ubiquitination machinery impacting gastrointestinal malignancies.Cell death & disease · 2024Review
- ASpedia-R: a package to retrieve junction-incorporating features and knowledge-based functions of human alternative splicing events.Bioinformatics advances · 2024Article
- Nanopore sequencing unveils the complexity of the cold-activated murine brown adipose tissue transcriptome.iScience · 2023Article
- Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage.Nature computational science · 2023Article
- Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage.bioRxiv : the preprint server for biology · 2023Article
- Advances in alternative splicing identification: deep learning and pantranscriptome.Frontiers in plant science · 2023Article
- Base Editing of Human Hematopoietic Stem Cells.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Analysis of matched primary and recurrent BRCA1/2 mutation-associated tumors identifies recurrence-specific drivers.Nature communications · 2022Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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Abstract
backgroundRNA-seq data is currently underutilized, in part because it is difficult to predict the functional impact of alternate transcription events. Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential.
resultsspliceR uses the full-length transcript output from RNA-seq assemblers to detect single or multiple exon skipping, alternative donor and acceptor sites, intron retention, alternative first or last exon usage, and mutually exclusive exon events. For each of these events spliceR also annotates the genomic coordinates of the differentially spliced elements, facilitating downstream sequence analysis. For each transcript isoform fraction values are calculated to identify transcript switching between conditions. Lastly, spliceR predicts the coding potential, as well as the potential nonsense mediated decay (NMD) sensitivity of each transcript.
conclusionsspliceR is an easy-to-use tool that extends the usability of RNA-seq and assembly technologies by allowing greater depth of annotation of RNA-seq data. spliceR is implemented as an R package and is freely available from the Bioconductor repository ( http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html).
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