ArticleRNA (New York, N.Y.)2023
Nanoblot: an R-package for visualization of RNA isoforms from long-read RNA-sequencing data.
Article in RNA (New York, N.Y.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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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.
The trial behind it
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
9 citing papers in PubMed.
- Direct RNA-seq provides evidence for an antiterminator function of the yeast Hrp1 protein on RNA polymerase II transcripts.RNA (New York, N.Y.) · 2026Article
- The RNA exosome maintains cellular RNA homeostasis by controlling transcript abundance in the brain.Cell reports · 2026Article
- A dual context-aware basecaller for nanopore direct RNA sequencing.Nature communications · 2026Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Direct RNA-seq provides evidence for an antiterminator function of the yeast Hrp1 protein on RNA polymerase II transcripts.bioRxiv : the preprint server for biology · 2025Article
- Transcription termination promotes splicing efficiency and fidelity in a compact genome.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Detection of Nuclear RNA Decay Intermediates Using a Modified Oxford Nanopore RNA Sequencing Strategy.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Widespread 3'UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites.BMC biology · 2024Article
- The MTR4/hnRNPK complex surveils aberrant polyadenylated RNAs with multiple exons.Nature communications · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
RT-PCR and northern blots have long been used to study RNA isoforms usage for single genes. Recent advancements in long-read sequencing have yielded unprecedented information about the usage and abundance of these RNA isoforms. However, visualization of long-read sequencing data remains challenging due to the high information density. To alleviate these issues, we have developed NanoBlot, an open-source R-package that generates northern blot and RT-PCR-like images from long-read sequencing data. NanoBlot requires aligned, positionally sorted and indexed BAM files. Plotting is based around ggplot2 and is easily customizable. Advantages of NanoBlot include a robust system for designing probes to visualize isoforms including excluding reads based on the presence or absence of a specified region, an elegant solution to representing isoforms with continuous variations in length, and the ability to overlay multiple genes in the same plot using different colors. We present examples of nanoblots compared to actual northern blot data. In addition to traditional gel-like images, the NanoBlot package can also output other visualizations such as violin plots and 3'-RACE-like plots focused on 3'-end isoforms visualization. The use of the NanoBlot package should provide a simple answer to some of the challenges of visualizing long-read RNA-sequencing data.
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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.