ArticleGigaScience2018
Clinker: visualizing fusion genes detected in RNA-seq data.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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.
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
11 citing papers in PubMed, 24 citations in OpenAlex.
- Unveiling the Genomic Symphony: Identification Cultivar-Specific Genes and Enhanced Insights on Sweet Sorghum Genomes Through Comprehensive superTranscriptomic Analysis.Journal of molecular evolution · 2024Article
- Ethanolamine metabolism through two genetically distinct loci enables Klebsiella pneumoniae to bypass nutritional competition in the gut.PLoS pathogens · 2024Article
- The Genetic Landscape of Antimicrobial Resistance Genes inAntibiotics (Basel, Switzerland) · 2024Article
- Optical genome mapping identifies a novel pediatric embryonal tumor with a ZNF532::NUTM1 fusion.The Journal of pathology · 2023Article
- TargetedCell reports methods · 2023Article
- Transcriptomic Harmonization as the Way for Suppressing Cross-Platform Bias and Batch Effect.Biomedicines · 2022Review
- Slinker: Visualising novel splicing events in RNA-Seq data.F1000Research · 2021Article
- Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology.Translational oncology · 2021Article
- MLL-TFE3: a novel and aggressive KMT2A fusion identified in infant leukemia.Blood advances · 2020Article
- The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia.Blood advances · 2020Article
- Clinker: visualizing fusion genes detected in RNA-seq data.GigaScience · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for identifying fusion genes from RNA-sequencing (RNA-seq) data, visualizing these transcripts and their supporting reads remains challenging. Findings: Clinker is a bioinformatics tool written in Python, R, and Bpipe that leverages the superTranscript method to visualize fusion genes. We demonstrate the use of Clinker to obtain interpretable visualizations of the RNA-seq data that lead to fusion calls. In addition, we use Clinker to explore multiple fusion transcripts with novel breakpoints within the P2RY8-CRLF2 fusion gene in B-cell acute lymphoblastic leukemia. Conclusions: Clinker is freely available software that allows visualization of fusion genes and the RNA-seq data used in their discovery.
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What OpenQuestion holds
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.