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Introduction to R01:11

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R is a powerful software environment for statistical computing and graphics. Originating as an implementation of the S language, developed at Bell Laboratories, R has evolved into a robust, open-source statistical software favored by statisticians and data scientists worldwide. Its comprehensive suite includes data manipulation, calculation, and graphical display capabilities, making it versatile for data analysis and visualization. Its programming language is at the core of R's...
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RNA Structure01:19

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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R chart, or range chart, is a fundamental tool in statistical process control used to monitor the variability within a process. It complements the X-bar (x̄) chart by focusing on the range of the data, rather than individual values, providing a clear picture of the process dispersion over time.
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R-chie: a web server and R package for visualizing cis and trans RNA-RNA, RNA-DNA and DNA-DNA interactions.

Volodymyr Tsybulskyi1,2, Mohamed Mounir1, Irmtraud M Meyer1,3

  • 1Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany.

Nucleic Acids Research
|September 25, 2020
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Summary

R-chie is a new tool for visualizing RNA-RNA, RNA-DNA, and DNA-DNA interactions across the transcriptome and genome. It offers advanced features for integrating evolutionary and quantitative data, aiding biological discovery.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Understanding biological interactions is crucial for deciphering functional roles.
  • Recent advances focus on trans-RNA-RNA, RNA-DNA, and trans-DNA-DNA interactions.
  • Visual inspection of integrated data aids biological insights.

Purpose of the Study:

  • To present R-chie, a web server and R package for visualizing molecular interactions.
  • To extend R-chie's capabilities for comprehensive cis and trans interaction visualization.
  • To provide tools for integrating diverse data types, including evolutionary and quantitative information.

Main Methods:

  • Development of a revised and extended R-chie web server and R package (R4RNA).
  • Implementation of visualization for cis and trans RNA-RNA, RNA-DNA, and DNA-DNA interactions.
  • Integration of features for incorporating evolutionary data (e.g., multiple sequence alignments) and quantitative data.

Main Results:

  • R-chie now visualizes cis and trans RNA-RNA, RNA-DNA, and DNA-DNA interactions.
  • The tool incorporates evolutionary information and quantitative data for enhanced analysis.
  • R-chie is accessible as a web server and a local R package (R4RNA).

Conclusions:

  • R-chie provides a unique platform for visualizing diverse molecular interactions.
  • The tool facilitates deeper understanding of biological functional roles through integrated data visualization.
  • R-chie supports both web-based and local analyses for broad accessibility.