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ReadXplorer
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ReadXplorer

ReadXplorer is a tool for visualization of genomic and transcriptomic mapped data. The ReadXplorer algorithm has functions for computing quality and quantity of alignments for classification, single nucleotide polymorphism (SNP) and transcription start site (TSS) detection, differential expression analysis, and transcriptome identification.



ReadXplorer

ReadXplorer is a tool for visualization of genomic and transcriptomic mapped data. The ReadXplorer algorithm has functions for computing quality and quantity of alignments for classification, single nucleotide polymorphism (SNP) and transcription start site (TSS) detection, differential expression analysis, and transcriptome identification.

Topic

Transcriptomics; Structural genomics; Comparative genomics

Details

  • Operation: Sequence visualisation
  • Input: GFF, FASTA, SAM, BAM
  • Output: -
  • Software interface: Web user interface
  • Language: Java
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v2
    • Cost: Free
  • Version name: -
    • Maturity: Mature
  • Credit: German Center for Infection Research (DZIF), Bundesministerium für Bildung und Forschung (BMBF), CLIB-Graduate Cluster Industrial Biotechnology, Ministry of Innovation of North Rhine-Westphalia, Ministry of Innovation of North Rhine-Westphalia, LOEWE focus group Medical RNomics (State of Hessen, Germany), Deutsche Forschungsgemeinschaft (DFG).
  • Contact: readxplorer _at_ computational.bio.uni-giessen.de
  • Collection: -

Publications

Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A "ReadXplorer--visualization and analysis of mapped sequences." Bioinformatics. 2014 Aug 15;30(16):2247-54. Epub 2014 Apr 30. https://doi.org/10.1093/bioinformatics/btu205
PMID: 24790157
PMCID: PMC4217279


Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A "ReadXplorer 2-detailed read mapping analysis and visualization from one single source." Bioinformatics. 2016 Dec 15;32(24):3702-3708. Epub 2016 Aug 18. https://doi.org/10.1093/bioinformatics/btw541
PMID: 27540267
PMCID: PMC5167064


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