ArticleGenome biology2019
ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Spider venom peptides with unique fold selectively block Shaker-type potassium channels.Cellular and molecular life sciences : CMLS · 2025Article
- Restrander: rapid orientation and artefact removal for long-read cDNA data.NAR genomics and bioinformatics · 2023Article
- High-sensitive spatially resolved T cell receptor sequencing with SPTCR-seq.Nature communications · 2023Article
- Omics Data and Data Representations for Deep Learning-Based Predictive Modeling.International journal of molecular sciences · 2022Review
- RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing.Genome biology · 2022Article
- ScisorWiz: visualizing differential isoform expression in single-cell long-read data.Bioinformatics (Oxford, England) · 2022Article
- Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis.Nature communications · 2021Article
- ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning.Genome biology · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe ReorientExpress, a method to perform reference-free orientation of transcriptomic long sequencing reads. ReorientExpress uses deep learning to correctly predict the orientation of the majority of reads, and in particular when trained on a closely related species or in combination with read clustering. ReorientExpress enables long-read transcriptomics in non-model organisms and samples without a genome reference without using additional technologies and is available at https://github.com/comprna/reorientexpress.
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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.