ArticleBioinformatics (Oxford, England)2016
ReadXplorer 2-detailed read mapping analysis and visualization from one single source.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 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.
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Who cites it
56 citing papers in PubMed.
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- An unusual glycerol-3-phosphate dehydrogenase in Sulfolobus acidocaldarius elucidates the diversity of glycerol metabolism across Archaea.Communications biology · 2025Article
- CRISPR-Cas9-driven genome editing inFrontiers in microbiology · 2025Article
- Sigma Factor Engineering inMicroorganisms · 2024Article
- Enhanced protein secretion in reduced genome strains of Streptomyces lividans.Microbial cell factories · 2024Article
- Discovery and overproduction of novel highly bioactive pamamycins through transcriptional engineering of the biosynthetic gene cluster.Microbial cell factories · 2023Article
- Systems biology of industrial oxytetracycline production in Streptomyces rimosus: the secrets of a mutagenized hyperproducer.Microbial cell factories · 2023Article
- Characterization of Bacterial Transcriptional Regulatory Networks inMicroorganisms · 2023Article
- Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis.Nucleic acids research · 2022Article
- Comparative analysis of Listeria monocytogenes plasmid transcriptomes reveals common and plasmid-specific gene expression patterns and high expression of noncoding RNAs.MicrobiologyOpen · 2022Article
- Overlapping SigH and SigE sigma factor regulons inFrontiers in microbiology · 2022Article
- Establishment of a near-contiguous genome sequence of the citric acid producing yeastNAR genomics and bioinformatics · 2021Article
- The two-Cys-type TetR repressor GbaA confers resistance under disulfide and electrophile stress in Staphylococcus aureus.Free radical biology & medicine · 2021Article
- Activation and Identification of a Griseusin Cluster inMolecules (Basel, Switzerland) · 2021Article
- Functional Redundancy and Specialization of the Conserved Cold Shock Proteins inMicroorganisms · 2021Article
- Superior production of heavy pamamycin derivatives using a bkdR deletion mutant of Streptomyces albus J1074/R2.Microbial cell factories · 2021Article
- Adaptive laboratory evolution accelerated glutarate production by Corynebacterium glutamicum.Microbial cell factories · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe vast amount of already available and currently generated read mapping data requires comprehensive visualization, and should benefit from bioinformatics tools offering a wide spectrum of analysis functionality from just one source. Appropriate handling of multiple mapped reads during mapping analyses remains an issue that demands improvement.
resultsThe capabilities of the read mapping analysis and visualization tool ReadXplorer were vastly enhanced. Here, we present an even finer granulated read mapping classification, improving the level of detail for analyses and visualizations. The spectrum of automatic analysis functions has been broadened to include genome rearrangement detection as well as correlation analysis between two mapping data sets. Existing functions were refined and enhanced, namely the computation of differentially expressed genes, the read count and normalization analysis and the transcription start site detection. Additionally, ReadXplorer 2 features a highly improved support for large eukaryotic data sets and a command line version, enabling its integration into workflows. Finally, the new version is now able to display any kind of tabular results from other bioinformatics tools. AVAILABILITY AND IMPLEMENTATION: http://www.readxplorer.org CONTACT: readxplorer@computational.bio.uni-giessen.deSupplementary information: Supplementary data are available at Bioinformatics online.
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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.